From 8a6ed3dec7e39bdfc7c1c32659f0dfb18f91149a Mon Sep 17 00:00:00 2001
From: mbsantiago <santiago.mbal@gmail.com>
Date: Thu, 24 Apr 2025 00:20:30 +0100
Subject: [PATCH] Starting to add logging to preprocess

---
 batdetect2/cli/train.py                   | 25 +++++++++++++++++++----
 batdetect2/data/annotations/batdetect2.py | 22 +++++++++++++++++++-
 batdetect2/data/datasets.py               |  6 ++++++
 3 files changed, 48 insertions(+), 5 deletions(-)

diff --git a/batdetect2/cli/train.py b/batdetect2/cli/train.py
index a55ea0d..2c7ebd3 100644
--- a/batdetect2/cli/train.py
+++ b/batdetect2/cli/train.py
@@ -2,6 +2,7 @@ from pathlib import Path
 from typing import Optional
 
 import click
+from loguru import logger
 
 from batdetect2.cli.base import cli
 from batdetect2.data import load_dataset_from_config
@@ -123,7 +124,7 @@ def train(): ...
 def preprocess(
     dataset_config: Path,
     output: Path,
-    target_config: Path,
+    target_config: Optional[Path] = None,
     base_dir: Optional[Path] = None,
     preprocess_config: Optional[Path] = None,
     label_config: Optional[Path] = None,
@@ -134,8 +135,13 @@ def preprocess(
     label_config_field: Optional[str] = None,
     dataset_field: Optional[str] = None,
 ):
+    logger.info("Starting preprocessing.")
+
     output = Path(output)
+    logger.info("Will save outputs to {output}", output=output)
+
     base_dir = base_dir or Path.cwd()
+    logger.debug("Current working directory: {base_dir}", base_dir=base_dir)
 
     preprocess = (
         load_preprocessing_config(
@@ -146,9 +152,13 @@ def preprocess(
         else None
     )
 
-    target = load_target_config(
-        target_config,
-        field=target_config_field,
+    target = (
+        load_target_config(
+            target_config,
+            field=target_config_field,
+        )
+        if target_config
+        else None
     )
 
     label = (
@@ -166,13 +176,20 @@ def preprocess(
         base_dir=base_dir,
     )
 
+    logger.info(
+        "Loaded {num_examples} annotated clips from the configured dataset",
+        num_examples=len(dataset),
+    )
+
     targets = build_targets(config=target)
     preprocessor = build_preprocessor(config=preprocess)
     labeller = build_clip_labeler(targets, config=label)
 
     if not output.exists():
+        logger.debug("Creating directory {directory}", directory=output)
         output.mkdir(parents=True)
 
+    logger.info("Will start preprocessing")
     preprocess_annotations(
         dataset,
         output_dir=output,
diff --git a/batdetect2/data/annotations/batdetect2.py b/batdetect2/data/annotations/batdetect2.py
index 055d84b..fe5697a 100644
--- a/batdetect2/data/annotations/batdetect2.py
+++ b/batdetect2/data/annotations/batdetect2.py
@@ -29,6 +29,7 @@ import os
 from pathlib import Path
 from typing import Literal, Optional, Union
 
+from loguru import logger
 from pydantic import Field, ValidationError
 from soundevent import data
 
@@ -177,6 +178,11 @@ def load_batdetect2_files_annotated_dataset(
         path = base_dir / path
 
     paths = list_file_annotations(path)
+    logger.debug(
+        "Found {num_files} files in the annotations directory {path}",
+        num_files=len(paths),
+        path=path,
+    )
 
     annotations = []
 
@@ -184,6 +190,7 @@ def load_batdetect2_files_annotated_dataset(
         try:
             file_annotation = load_file_annotation(p)
         except (FileNotFoundError, ValidationError):
+            logger.warning("Could not load annotations in file {path}", path=p)
             continue
 
         if (
@@ -191,6 +198,10 @@ def load_batdetect2_files_annotated_dataset(
             and dataset.filter.only_annotated
             and not file_annotation.annotated
         ):
+            logger.debug(
+                "Annotation in file {path} omited: not annotated",
+                path=p,
+            )
             continue
 
         if (
@@ -198,6 +209,10 @@ def load_batdetect2_files_annotated_dataset(
             and dataset.filter.exclude_issues
             and file_annotation.issues
         ):
+            logger.debug(
+                "Annotation in file {path} omited: has issues",
+                path=p,
+            )
             continue
 
         try:
@@ -205,7 +220,12 @@ def load_batdetect2_files_annotated_dataset(
                 file_annotation,
                 audio_dir=audio_dir,
             )
-        except FileNotFoundError:
+        except FileNotFoundError as err:
+            logger.warning(
+                "Did not find the audio related to the annotation file {path}. Error: {err}",
+                path=p,
+                err=err,
+            )
             continue
 
         annotations.append(
diff --git a/batdetect2/data/datasets.py b/batdetect2/data/datasets.py
index f0e3278..b960305 100644
--- a/batdetect2/data/datasets.py
+++ b/batdetect2/data/datasets.py
@@ -21,6 +21,7 @@ The core components are:
 from pathlib import Path
 from typing import Annotated, List, Optional
 
+from loguru import logger
 from pydantic import Field
 from soundevent import data, io
 
@@ -115,6 +116,11 @@ def load_dataset(
     clip_annotations = []
     for source in dataset.sources:
         annotated_source = load_annotated_dataset(source, base_dir=base_dir)
+        logger.debug(
+            "Loaded {num_examples} from dataset source '{source_name}'",
+            num_examples=len(annotated_source.clip_annotations),
+            source_name=source.name,
+        )
         clip_annotations.extend(
             insert_source_tag(clip_annotation, source)
             for clip_annotation in annotated_source.clip_annotations