birdnet-analyzer 2.0.1__tar.gz → 2.1.0__tar.gz

{birdnet_analyzer-2.0.1 → birdnet_analyzer-2.1.0}/BirdNET_Analyzer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: birdnet_analyzer
-Version: 2.0.1
+Version: 2.1.0
 Summary: BirdNET analyzer for scientific audio data processing and bird classification.
 Author: Stefan Kahl
 Maintainer: Josef Haupt, Max Mauermann
@@ -25,6 +25,8 @@ Requires-Dist: resampy
 Requires-Dist: tensorflow==2.15.1
 Requires-Dist: scikit-learn==1.6.1
 Requires-Dist: tqdm
+Requires-Dist: pandas
+Requires-Dist: matplotlib
 Provides-Extra: train
 Requires-Dist: keras-tuner; extra == "train"
 Provides-Extra: server
@@ -32,21 +34,25 @@ Requires-Dist: bottle; extra == "server"
 Requires-Dist: requests; extra == "server"
 Provides-Extra: gui
 Requires-Dist: birdnet-analyzer[embeddings,train]; extra == "gui"
-Requires-Dist: gradio==5.25.2; extra == "gui"
+Requires-Dist: gradio==5.32.1; extra == "gui"
 Requires-Dist: pywebview; extra == "gui"
-Requires-Dist: matplotlib; extra == "gui"
 Requires-Dist: plotly[express]; extra == "gui"
-Requires-Dist: seaborn; extra == "gui"
 Requires-Dist: pywin32; platform_system == "Windows" and extra == "gui"
+Requires-Dist: qtpy; platform_system == "Linux" and extra == "gui"
+Requires-Dist: PyGObject; platform_system == "Linux" and extra == "gui"
 Provides-Extra: embeddings
 Requires-Dist: perch-hoplite; extra == "embeddings"
 Provides-Extra: all
 Requires-Dist: birdnet-analyzer[gui,server]; extra == "all"
+Provides-Extra: docs
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: sphinx-rtd-theme; extra == "docs"
+Requires-Dist: sphinx-argparse; extra == "docs"
+Provides-Extra: tests
+Requires-Dist: pytest; extra == "tests"
 Provides-Extra: dev
-Requires-Dist: sphinx; extra == "dev"
-Requires-Dist: sphinx-rtd-theme; extra == "dev"
-Requires-Dist: sphinx-argparse; extra == "dev"
-Requires-Dist: pytest; extra == "dev"
+Requires-Dist: birdnet_analyzer[tests]; extra == "dev"
+Requires-Dist: birdnet_analyzer[docs]; extra == "dev"
 Requires-Dist: ruff; extra == "dev"
 Dynamic: license-file
 
@@ -72,9 +78,11 @@ Dynamic: license-file
 [![GitHub release](https://img.shields.io/github/v/release/birdnet-team/BirdNET-Analyzer)](https://github.com/birdnet-team/BirdNET-Analyzer/releases/latest)
 [![PyPI - Version](https://img.shields.io/pypi/v/birdnet_analyzer?logo=pypi)](https://pypi.org/project/birdnet-analyzer/)
 
+[![Sponsor](https://img.shields.io/badge/Support%20our%20work-8A2BE2?logo=data:image/svg+xml;base64,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)](https://give.birds.cornell.edu/page/132162/donate/1)
+
 </div>
 
-This repo contains BirdNET models and scripts for processing large amounts of audio data or single audio files.
+This repo contains BirdNET scripts for processing large amounts of audio data or single audio files.
 This is the most advanced version of BirdNET for acoustic analyses and we will keep this repository up-to-date with new models and improved interfaces to enable scientists with no CS background to run the analysis.
 
 Feel free to use BirdNET for your acoustic analyses and research.
@@ -99,6 +107,7 @@ You can access documentation for this project [here](https://birdnet-team.github
 ## Download
 
 You can download installers for Windows and macOS from the [releases page](https://github.com/birdnet-team/BirdNET-Analyzer/releases/latest).
+Models can be found on [Zenodo](https://zenodo.org/records/15050749).
 
 ## About
 

{birdnet_analyzer-2.0.1 → birdnet_analyzer-2.1.0}/BirdNET_Analyzer.egg-info/SOURCES.txt

@@ -11,7 +11,7 @@ birdnet_analyzer/__init__.py
 birdnet_analyzer/audio.py
 birdnet_analyzer/cli.py
 birdnet_analyzer/config.py
-birdnet_analyzer/eBird_taxonomy_codes_2021E.json
+birdnet_analyzer/eBird_taxonomy_codes_2024E.json
 birdnet_analyzer/model.py
 birdnet_analyzer/playground.py
 birdnet_analyzer/translate.py
@@ -131,4 +131,5 @@ birdnet_analyzer/train/__init__.py
 birdnet_analyzer/train/__main__.py
 birdnet_analyzer/train/cli.py
 birdnet_analyzer/train/core.py
-birdnet_analyzer/train/utils.py
+birdnet_analyzer/train/utils.py
+tests/test_utils.py

{birdnet_analyzer-2.0.1 → birdnet_analyzer-2.1.0}/BirdNET_Analyzer.egg-info/requires.txt

@@ -3,27 +3,34 @@ resampy
 tensorflow==2.15.1
 scikit-learn==1.6.1
 tqdm
+pandas
+matplotlib
 
 [all]
 birdnet-analyzer[gui,server]
 
 [dev]
+birdnet_analyzer[tests]
+birdnet_analyzer[docs]
+ruff
+
+[docs]
 sphinx
 sphinx-rtd-theme
 sphinx-argparse
-pytest
-ruff
 
 [embeddings]
 perch-hoplite
 
 [gui]
 birdnet-analyzer[embeddings,train]
-gradio==5.25.2
+gradio==5.32.1
 pywebview
-matplotlib
 plotly[express]
-seaborn
+
+[gui:platform_system == "Linux"]
+qtpy
+PyGObject
 
 [gui:platform_system == "Windows"]
 pywin32
@@ -32,5 +39,8 @@ pywin32
 bottle
 requests
 
+[tests]
+pytest
+
 [train]
 keras-tuner

{birdnet_analyzer-2.0.1 → birdnet_analyzer-2.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: birdnet_analyzer
-Version: 2.0.1
+Version: 2.1.0
 Summary: BirdNET analyzer for scientific audio data processing and bird classification.
 Author: Stefan Kahl
 Maintainer: Josef Haupt, Max Mauermann
@@ -25,6 +25,8 @@ Requires-Dist: resampy
 Requires-Dist: tensorflow==2.15.1
 Requires-Dist: scikit-learn==1.6.1
 Requires-Dist: tqdm
+Requires-Dist: pandas
+Requires-Dist: matplotlib
 Provides-Extra: train
 Requires-Dist: keras-tuner; extra == "train"
 Provides-Extra: server
@@ -32,21 +34,25 @@ Requires-Dist: bottle; extra == "server"
 Requires-Dist: requests; extra == "server"
 Provides-Extra: gui
 Requires-Dist: birdnet-analyzer[embeddings,train]; extra == "gui"
-Requires-Dist: gradio==5.25.2; extra == "gui"
+Requires-Dist: gradio==5.32.1; extra == "gui"
 Requires-Dist: pywebview; extra == "gui"
-Requires-Dist: matplotlib; extra == "gui"
 Requires-Dist: plotly[express]; extra == "gui"
-Requires-Dist: seaborn; extra == "gui"
 Requires-Dist: pywin32; platform_system == "Windows" and extra == "gui"
+Requires-Dist: qtpy; platform_system == "Linux" and extra == "gui"
+Requires-Dist: PyGObject; platform_system == "Linux" and extra == "gui"
 Provides-Extra: embeddings
 Requires-Dist: perch-hoplite; extra == "embeddings"
 Provides-Extra: all
 Requires-Dist: birdnet-analyzer[gui,server]; extra == "all"
+Provides-Extra: docs
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: sphinx-rtd-theme; extra == "docs"
+Requires-Dist: sphinx-argparse; extra == "docs"
+Provides-Extra: tests
+Requires-Dist: pytest; extra == "tests"
 Provides-Extra: dev
-Requires-Dist: sphinx; extra == "dev"
-Requires-Dist: sphinx-rtd-theme; extra == "dev"
-Requires-Dist: sphinx-argparse; extra == "dev"
-Requires-Dist: pytest; extra == "dev"
+Requires-Dist: birdnet_analyzer[tests]; extra == "dev"
+Requires-Dist: birdnet_analyzer[docs]; extra == "dev"
 Requires-Dist: ruff; extra == "dev"
 Dynamic: license-file
 
@@ -72,9 +78,11 @@ Dynamic: license-file
 [![GitHub release](https://img.shields.io/github/v/release/birdnet-team/BirdNET-Analyzer)](https://github.com/birdnet-team/BirdNET-Analyzer/releases/latest)
 [![PyPI - Version](https://img.shields.io/pypi/v/birdnet_analyzer?logo=pypi)](https://pypi.org/project/birdnet-analyzer/)
 
+[![Sponsor](https://img.shields.io/badge/Support%20our%20work-8A2BE2?logo=data:image/svg+xml;base64,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)](https://give.birds.cornell.edu/page/132162/donate/1)
+
 </div>
 
-This repo contains BirdNET models and scripts for processing large amounts of audio data or single audio files.
+This repo contains BirdNET scripts for processing large amounts of audio data or single audio files.
 This is the most advanced version of BirdNET for acoustic analyses and we will keep this repository up-to-date with new models and improved interfaces to enable scientists with no CS background to run the analysis.
 
 Feel free to use BirdNET for your acoustic analyses and research.
@@ -99,6 +107,7 @@ You can access documentation for this project [here](https://birdnet-team.github
 ## Download
 
 You can download installers for Windows and macOS from the [releases page](https://github.com/birdnet-team/BirdNET-Analyzer/releases/latest).
+Models can be found on [Zenodo](https://zenodo.org/records/15050749).
 
 ## About
 

{birdnet_analyzer-2.0.1 → birdnet_analyzer-2.1.0}/README.md

@@ -20,9 +20,11 @@
 [![GitHub release](https://img.shields.io/github/v/release/birdnet-team/BirdNET-Analyzer)](https://github.com/birdnet-team/BirdNET-Analyzer/releases/latest)
 [![PyPI - Version](https://img.shields.io/pypi/v/birdnet_analyzer?logo=pypi)](https://pypi.org/project/birdnet-analyzer/)
 
+[![Sponsor](https://img.shields.io/badge/Support%20our%20work-8A2BE2?logo=data:image/svg+xml;base64,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)](https://give.birds.cornell.edu/page/132162/donate/1)
+
 </div>
 
-This repo contains BirdNET models and scripts for processing large amounts of audio data or single audio files.
+This repo contains BirdNET scripts for processing large amounts of audio data or single audio files.
 This is the most advanced version of BirdNET for acoustic analyses and we will keep this repository up-to-date with new models and improved interfaces to enable scientists with no CS background to run the analysis.
 
 Feel free to use BirdNET for your acoustic analyses and research.
@@ -47,6 +49,7 @@ You can access documentation for this project [here](https://birdnet-team.github
 ## Download
 
 You can download installers for Windows and macOS from the [releases page](https://github.com/birdnet-team/BirdNET-Analyzer/releases/latest).
+Models can be found on [Zenodo](https://zenodo.org/records/15050749).
 
 ## About
 

birdnet_analyzer-2.1.0/birdnet_analyzer/analyze/__init__.py

@@ -0,0 +1,19 @@
+import os
+
+import birdnet_analyzer.config as cfg
+from birdnet_analyzer.analyze.core import analyze
+
+POSSIBLE_ADDITIONAL_COLUMNS_MAP = {
+    "lat": lambda: cfg.LATITUDE,
+    "lon": lambda: cfg.LONGITUDE,
+    "week": lambda: cfg.WEEK,
+    "overlap": lambda: cfg.SIG_OVERLAP,
+    "sensitivity": lambda: cfg.SIGMOID_SENSITIVITY,
+    "min_conf": lambda: cfg.MIN_CONFIDENCE,
+    "species_list": lambda: cfg.SPECIES_LIST_FILE or "",
+    "model": lambda: os.path.basename(cfg.MODEL_PATH),
+}
+
+__all__ = [
+    "analyze",
+]

{birdnet_analyzer-2.0.1 → birdnet_analyzer-2.1.0}/birdnet_analyzer/analyze/cli.py

@@ -22,4 +22,9 @@ def main():
     except Exception:
         pass
 
+    if "additional_columns" in args and args.additional_columns and "csv" not in args.rtype:
+        import warnings
+
+        warnings.warn("The --additional_columns argument is only valid for CSV output. It will be ignored.", stacklevel=1)
+
     analyze(**vars(args))

{birdnet_analyzer-2.0.1 → birdnet_analyzer-2.1.0}/birdnet_analyzer/analyze/core.py

@@ -26,6 +26,7 @@ def analyze(
     merge_consecutive: int = 1,
     threads: int = 8,
     locale: str = "en",
+    additional_columns: list[str] | None = None,
 ):
     """
     Analyzes audio files for bird species detection using the BirdNET-Analyzer.
@@ -53,6 +54,7 @@ def analyze(
         merge_consecutive (int, optional): Merge consecutive detections within this time window in seconds. Defaults to 1.
         threads (int, optional): Number of CPU threads to use for analysis. Defaults to 8.
         locale (str, optional): Locale for species names and output. Defaults to "en".
+        additional_columns (list[str] | None, optional): Additional columns to include in the output. Defaults to None.
     Returns:
         None
     Raises:
@@ -95,6 +97,7 @@ def analyze(
         skip_existing_results=skip_existing_results,
         threads=threads,
         labels_file=cfg.LABELS_FILE,
+        additional_columns=additional_columns,
     )
 
     print(f"Found {len(cfg.FILE_LIST)} files to analyze")
@@ -150,6 +153,7 @@ def _set_params(
     merge_consecutive,
     threads,
     labels_file=None,
+    additional_columns=None,
 ):
     import birdnet_analyzer.config as cfg
     from birdnet_analyzer.analyze.utils import load_codes
@@ -162,7 +166,7 @@ def _set_params(
     cfg.LOCATION_FILTER_THRESHOLD = sf_thresh
     cfg.TOP_N = top_n
     cfg.MERGE_CONSECUTIVE = merge_consecutive
-    cfg.INPUT_PATH = audio_input
+    cfg.INPUT_PATH = audio_input.replace("/", os.sep)
     cfg.MIN_CONFIDENCE = min_conf
     cfg.SIGMOID_SENSITIVITY = sensitivity
     cfg.SIG_OVERLAP = overlap
@@ -172,6 +176,7 @@ def _set_params(
     cfg.RESULT_TYPES = rtype
     cfg.COMBINE_RESULTS = combine_results
     cfg.BATCH_SIZE = bs
+    cfg.ADDITIONAL_COLUMNS = additional_columns
 
     if not output:
         if os.path.isfile(cfg.INPUT_PATH):

{birdnet_analyzer-2.0.1 → birdnet_analyzer-2.1.0}/birdnet_analyzer/analyze/utils.py

@@ -4,17 +4,17 @@ import datetime
 import json
 import operator
 import os
+from collections.abc import Sequence
 
 import numpy as np
 
 import birdnet_analyzer.config as cfg
 from birdnet_analyzer import audio, model, utils
 
-RAVEN_TABLE_HEADER = "Selection\tView\tChannel\tBegin Time (s)\tEnd Time (s)\tLow Freq (Hz)\tHigh Freq (Hz)\tCommon Name\tSpecies Code\tConfidence\tBegin Path\tFile Offset (s)\n"  # noqa: E501
-RTABLE_HEADER = "filepath,start,end,scientific_name,common_name,confidence,lat,lon,week,overlap,sensitivity,min_conf,species_list,model\n"
-KALEIDOSCOPE_HEADER = (
-    "INDIR,FOLDER,IN FILE,OFFSET,DURATION,scientific_name,common_name,confidence,lat,lon,week,overlap,sensitivity\n"
+RAVEN_TABLE_HEADER = (
+    "Selection\tView\tChannel\tBegin Time (s)\tEnd Time (s)\tLow Freq (Hz)\tHigh Freq (Hz)\tCommon Name\tSpecies Code\tConfidence\tBegin Path\tFile Offset (s)\n"
 )
+KALEIDOSCOPE_HEADER = "INDIR,FOLDER,IN FILE,OFFSET,DURATION,scientific_name,common_name,confidence,lat,lon,week,overlap,sensitivity\n"
 CSV_HEADER = "Start (s),End (s),Scientific name,Common name,Confidence,File\n"
 SCRIPT_DIR = os.path.abspath(os.path.dirname(__file__))
 
@@ -80,7 +80,7 @@ def generate_raven_table(timestamps: list[str], result: dict[str, list], afile_p
 
     high_freq = min(high_freq, int(cfg.SIG_FMAX / cfg.AUDIO_SPEED))
 
-    high_freq = min(high_freq, int(cfg.BANDPASS_FMAX / cfg.AUDIO_SPEED))
+    high_freq = int(min(high_freq, int(cfg.BANDPASS_FMAX / cfg.AUDIO_SPEED)))
     low_freq = max(cfg.SIG_FMIN, int(cfg.BANDPASS_FMIN / cfg.AUDIO_SPEED))
 
     # Extract valid predictions for every timestamp
@@ -92,7 +92,9 @@ def generate_raven_table(timestamps: list[str], result: dict[str, list], afile_p
             selection_id += 1
             label = cfg.TRANSLATED_LABELS[cfg.LABELS.index(c[0])]
             code = cfg.CODES[c[0]] if c[0] in cfg.CODES else c[0]
-            rstring += f"{selection_id}\tSpectrogram 1\t1\t{start}\t{end}\t{low_freq}\t{high_freq}\t{label.split('_', 1)[-1]}\t{code}\t{c[1]:.4f}\t{afile_path}\t{start}\n"  # noqa: E501
+            rstring += (
+                f"{selection_id}\tSpectrogram 1\t1\t{start}\t{end}\t{low_freq}\t{high_freq}\t{label.split('_', 1)[-1]}\t{code}\t{c[1]:.4f}\t{afile_path}\t{start}\n"
+            )
 
         # Write result string to file
         out_string += rstring
@@ -103,9 +105,7 @@ def generate_raven_table(timestamps: list[str], result: dict[str, list], afile_p
     # of file durations during the analysis.
     if len(out_string) == len(RAVEN_TABLE_HEADER) and cfg.OUTPUT_PATH is not None:
         selection_id += 1
-        out_string += (
-            f"{selection_id}\tSpectrogram 1\t1\t0\t3\t{low_freq}\t{high_freq}\tnocall\tnocall\t1.0\t{afile_path}\t0\n"
-        )
+        out_string += f"{selection_id}\tSpectrogram 1\t1\t0\t3\t{low_freq}\t{high_freq}\tnocall\tnocall\t1.0\t{afile_path}\t0\n"
 
     utils.save_result_file(result_path, out_string)
 
@@ -202,7 +202,18 @@ def generate_csv(timestamps: list[str], result: dict[str, list], afile_path: str
     Returns:
         None
     """
+    from birdnet_analyzer.analyze import POSSIBLE_ADDITIONAL_COLUMNS_MAP
+
     out_string = CSV_HEADER
+    columns_map = {}
+
+    if cfg.ADDITIONAL_COLUMNS:
+        for col in cfg.ADDITIONAL_COLUMNS:
+            if col in POSSIBLE_ADDITIONAL_COLUMNS_MAP:
+                columns_map[col] = POSSIBLE_ADDITIONAL_COLUMNS_MAP[col]()
+
+        if columns_map:
+            out_string = out_string[:-1] + "," + ",".join(columns_map) + "\n"
 
     for timestamp in timestamps:
         rstring = ""
@@ -210,7 +221,12 @@ def generate_csv(timestamps: list[str], result: dict[str, list], afile_path: str
         for c in result[timestamp]:
             start, end = timestamp.split("-", 1)
             label = cfg.TRANSLATED_LABELS[cfg.LABELS.index(c[0])]
-            rstring += f"{start},{end},{label.split('_', 1)[0]},{label.split('_', 1)[-1]},{c[1]:.4f},{afile_path}\n"
+            rstring += f"{start},{end},{label.split('_', 1)[0]},{label.split('_', 1)[-1]},{c[1]:.4f},{afile_path}"
+
+            if columns_map:
+                rstring += "," + ",".join(str(val) for val in columns_map.values())
+
+            rstring += "\n"
 
         # Write result string to file
         out_string += rstring
@@ -364,29 +380,23 @@ def combine_csv_files(saved_results: list[str]):
     Args:
         saved_results (list[str]): A list of file paths to the CSV files to be combined.
     """
-    # Combine all files
-    with open(os.path.join(cfg.OUTPUT_PATH, cfg.OUTPUT_CSV_FILENAME), "w", encoding="utf-8") as f:
-        f.write(CSV_HEADER)
+    out_string = ""
 
-        for rfile in saved_results:
+    for rfile in saved_results:
+        try:
             with open(rfile, encoding="utf-8") as rf:
-                try:
-                    lines = rf.readlines()
+                lines = rf.readlines()
+                out_string += "".join(lines[1:] if out_string else lines)
 
-                    # make sure it's a selection table
-                    if "Start (s)" not in lines[0] or "Confidence" not in lines[0]:
-                        continue
-
-                    # skip header and add to file
-                    for line in lines[1:]:
-                        f.write(line)
+        except Exception as ex:
+            print(f"Error: Cannot combine results from {rfile}.\n", flush=True)
+            utils.write_error_log(ex)
 
-                except Exception as ex:
-                    print(f"Error: Cannot combine results from {rfile}.\n", flush=True)
-                    utils.write_error_log(ex)
+    with open(os.path.join(cfg.OUTPUT_PATH, cfg.OUTPUT_CSV_FILENAME), "w", encoding="utf-8") as f:
+        f.write(out_string)
 
 
-def combine_results(saved_results: list[dict[str, str]]):
+def combine_results(saved_results: Sequence[dict[str, str]| None]):
     """
     Combines various types of result files based on the configuration settings.
     This function checks the types of results specified in the configuration
@@ -403,9 +413,6 @@ def combine_results(saved_results: list[dict[str, str]]):
     if "table" in cfg.RESULT_TYPES:
         combine_raven_tables([f["table"] for f in saved_results if f])
 
-    # if "r" in cfg.RESULT_TYPES:
-    #     combine_rtable_files([f["r"] for f in saved_results if f])
-
     if "kaleidoscope" in cfg.RESULT_TYPES:
         combine_kaleidoscope_files([f["kaleidoscope"] for f in saved_results if f])
 
@@ -509,9 +516,7 @@ def get_raw_audio_from_file(fpath: str, offset, duration):
         The signal split into a list of chunks.
     """
     # Open file
-    sig, rate = audio.open_audio_file(
-        fpath, cfg.SAMPLE_RATE, offset, duration, cfg.BANDPASS_FMIN, cfg.BANDPASS_FMAX, cfg.AUDIO_SPEED
-    )
+    sig, rate = audio.open_audio_file(fpath, cfg.SAMPLE_RATE, offset, duration, cfg.BANDPASS_FMIN, cfg.BANDPASS_FMAX, cfg.AUDIO_SPEED)
 
     # Split into raw audio chunks
     return audio.split_signal(sig, rate, cfg.SIG_LENGTH, cfg.SIG_OVERLAP, cfg.SIG_MINLEN)
@@ -563,16 +568,14 @@ def get_result_file_names(fpath: str):
     # if "r" in cfg.RESULT_TYPES:
     #     result_names["r"] = os.path.join(cfg.OUTPUT_PATH, file_shorthand + ".BirdNET.results.r.csv")
     if "kaleidoscope" in cfg.RESULT_TYPES:
-        result_names["kaleidoscope"] = os.path.join(
-            cfg.OUTPUT_PATH, file_shorthand + ".BirdNET.results.kaleidoscope.csv"
-        )
+        result_names["kaleidoscope"] = os.path.join(cfg.OUTPUT_PATH, file_shorthand + ".BirdNET.results.kaleidoscope.csv")
     if "csv" in cfg.RESULT_TYPES:
         result_names["csv"] = os.path.join(cfg.OUTPUT_PATH, file_shorthand + ".BirdNET.results.csv")
 
     return result_names
 
 
-def analyze_file(item):
+def analyze_file(item) -> dict[str, str] | None:
     """
     Analyzes an audio file and generates prediction results.
 
@@ -606,7 +609,7 @@ def analyze_file(item):
     print(f"Analyzing {fpath}", flush=True)
 
     try:
-        fileLengthSeconds = int(audio.get_audio_file_length(fpath) / cfg.AUDIO_SPEED)
+        fileLengthSeconds = audio.get_audio_file_length(fpath)
     except Exception as ex:
         # Write error log
         print(f"Error: Cannot analyze audio file {fpath}. File corrupt?\n", flush=True)
@@ -649,8 +652,7 @@ def analyze_file(item):
                     p_labels = [
                         p
                         for p in zip(cfg.LABELS, pred, strict=True)
-                        if (cfg.TOP_N or p[1] >= cfg.MIN_CONFIDENCE)
-                        and (not cfg.SPECIES_LIST or p[0] in cfg.SPECIES_LIST)
+                        if (cfg.TOP_N or p[1] >= cfg.MIN_CONFIDENCE) and (not cfg.SPECIES_LIST or p[0] in cfg.SPECIES_LIST)
                     ]
 
                     # Sort by score

{birdnet_analyzer-2.0.1 → birdnet_analyzer-2.1.0}/birdnet_analyzer/audio.py

@@ -61,7 +61,7 @@ def get_audio_file_length(path):
     """
     # Open file with librosa (uses ffmpeg or libav)
 
-    return librosa.get_duration(filename=path, sr=None)
+    return librosa.get_duration(path=path, sr=None)
 
 
 def get_sample_rate(path: str):
@@ -184,7 +184,7 @@ def split_signal(sig, rate, seconds, overlap, minlen, amount=None):
 
     # Split signal with overlap
     sig_splits = []
-    sig_splits.extend(data[i : i + chunksize] for i in range(0, lastchunkpos, stepsize))
+    sig_splits.extend(data[i : i + chunksize] for i in range(0, lastchunkpos + 1, stepsize))
 
     return sig_splits
 

{birdnet_analyzer-2.0.1 → birdnet_analyzer-2.1.0}/birdnet_analyzer/cli.py

@@ -31,7 +31,7 @@ ASCII_LOGO = r"""
                                                  **=====        
                                                ***+==           
                                               ****+             
-""" # noqa: W291
+"""  # noqa: W291
 
 
 def io_args():
@@ -80,10 +80,9 @@ def bandpass_args():
 
     return p
 
-
-def species_args():
+def species_list_args():
     """
-    Creates an argument parser for species-related arguments.
+    Creates an argument parser for species-list arguments.
     Returns:
         argparse.ArgumentParser: The argument parser with the following arguments:
             --lat (float): Recording location latitude. Set -1 to ignore. Default is -1.
@@ -104,17 +103,33 @@ def species_args():
         default=-1,
         help="Week of the year when the recording was made. Values in [1, 48] (4 weeks per month). Set -1 for year-round species list.",
     )
-    p.add_argument(
-        "--slist",
-        help='Path to species list file or folder. If folder is provided, species list needs to be named "species_list.txt". If lat and lon are provided, this list will be ignored.',
-    )
     p.add_argument(
         "--sf_thresh",
         type=lambda a: max(0.0001, min(0.99, float(a))),
         default=cfg.LOCATION_FILTER_THRESHOLD,
         help="Minimum species occurrence frequency threshold for location filter. Values in [0.0001, 0.99].",
     )
+    return p
 
+def species_args():
+    """
+    Creates an argument parser for species-related arguments including the species-list arguments.
+    Returns:
+        argparse.ArgumentParser: The argument parser with the following arguments:
+            --lat (float): Recording location latitude. Set -1 to ignore. Default is -1.
+            --lon (float): Recording location longitude. Set -1 to ignore. Default is -1.
+            --week (int): Week of the year when the recording was made. Values in [1, 48] (4 weeks per month).
+                          Set -1 for year-round species list. Default is -1.
+            --sf_thresh (float): Minimum species occurrence frequency threshold for location filter. Values in [0.01, 0.99].
+                                 Defaults to cfg.LOCATION_FILTER_THRESHOLD.
+            --slist (str): Path to species list file or folder. If folder is provided, species list needs to be named
+                           "species_list.txt". If lat and lon are provided, this list will be ignored.
+    """
+    p = species_list_args()
+    p.add_argument(
+        "--slist",
+        help='Path to species list file or folder. If folder is provided, species list needs to be named "species_list.txt". If lat and lon are provided, this list will be ignored.',
+    )
     return p
 
 
@@ -309,6 +324,7 @@ def analyzer_parser():
     Returns:
         argparse.ArgumentParser: Configured argument parser for the BirdNET Analyzer CLI.
     """
+    from birdnet_analyzer.analyze import POSSIBLE_ADDITIONAL_COLUMNS_MAP
     parents = [
         io_args(),
         bandpass_args(),
@@ -339,6 +355,14 @@ def analyzer_parser():
         help="Specifies output format. Values in `['table', 'audacity',  'kaleidoscope', 'csv']`.",
         action=UniqueSetAction,
     )
+    parser.add_argument(
+        "--additional_columns",
+        choices=POSSIBLE_ADDITIONAL_COLUMNS_MAP.keys(),
+        nargs="+",
+        help="Additional columns to include in the output, only applied to the csv output format. "
+        + f"Values in [{','.join(POSSIBLE_ADDITIONAL_COLUMNS_MAP.keys())}].",
+        action=UniqueSetAction,
+    )
     parser.add_argument(
         "--combine_results",
         help="Also outputs a combined file for all the selected result types. If not set combined tables will be generated.",
@@ -404,6 +428,10 @@ def embeddings_parser():
         help="Path to input file or folder.",
     )
 
+    parser.add_argument(
+        "--file_output",
+    )
+
     return parser
 
 
@@ -498,9 +526,7 @@ def segments_parser():
     )
     parser.add_argument("audio_input", metavar="INPUT", help="Path to folder containing audio files.")
     parser.add_argument("-r", "--results", help="Path to folder containing result files. Defaults to the `input` path.")
-    parser.add_argument(
-        "-o", "--output", help="Output folder path for extracted segments. Defaults to the `input` path."
-    )
+    parser.add_argument("-o", "--output", help="Output folder path for extracted segments. Defaults to the `input` path.")
     parser.add_argument(
         "--max_segments",
         type=lambda a: max(1, int(a)),
@@ -535,9 +561,7 @@ def server_parser():
     parser.add_argument("-p", "--port", type=int, default=8080, help="Port of API endpoint server.")
     parser.add_argument(
         "--spath",
-        default="uploads/"
-        if os.environ.get("IS_GITHUB_RUNNER", "false").lower() == "true"
-        else os.path.join(SCRIPT_DIR, "uploads"),
+        default="uploads/" if os.environ.get("IS_GITHUB_RUNNER", "false").lower() == "true" else os.path.join(SCRIPT_DIR, "uploads"),
         help="Path to folder where uploaded files should be stored.",
     )
 
@@ -555,7 +579,7 @@ def species_parser():
     """
     parser = argparse.ArgumentParser(
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
-        parents=[species_args()],
+        parents=[species_list_args()],
     )
     parser.add_argument(
         "output",
@@ -603,9 +627,7 @@ def train_parser():
         metavar="INPUT",
         help="Path to training data folder. Subfolder names are used as labels.",
     )
-    parser.add_argument(
-        "--test_data", help="Path to test data folder. If not specified, a random validation split will be used."
-    )
+    parser.add_argument("--test_data", help="Path to test data folder. If not specified, a random validation split will be used.")
     parser.add_argument(
         "--crop_mode",
         default=cfg.SAMPLE_CROP_MODE,
@@ -633,6 +655,7 @@ def train_parser():
     )
     parser.add_argument(
         "--focal-loss",
+        dest="use_focal_loss",
         action="store_true",
         help="Use focal loss for training (helps with imbalanced classes and hard examples).",
     )