docs: expand python workflow tutorial

docs/source/reference/detections.md

@@ -0,0 +1,42 @@
+# Detections reference
+
+These are the main prediction objects returned by BatDetect2 inference methods.
+
+Defined in `batdetect2.postprocess.types`.
+
+## `ClipDetections`
+
+`ClipDetections` represents the predictions for one clip or one full recording.
+
+Fields:
+
+- `clip`
+  - the `soundevent` clip metadata for the processed audio.
+- `detections`
+  - list of `Detection` objects for that clip.
+
+## `Detection`
+
+`Detection` represents one detected event.
+
+Fields:
+
+- `geometry`
+  - time-frequency geometry for the detected event.
+- `detection_score`
+  - confidence that there is an event at this location.
+- `class_scores`
+  - class ranking scores for the detected event.
+- `features`
+  - per-detection feature vector from the model.
+
+## Related pages
+
+- Python tutorial:
+  {doc}`../tutorials/integrate-with-a-python-pipeline`
+- API reference:
+  {doc}`api`
+- What BatDetect2 predicts:
+  {doc}`../explanation/what-batdetect2-predicts`
+- Features and embeddings:
+  {doc}`../explanation/extracted-features-and-embeddings`

docs/source/reference/index.md

@@ -10,6 +10,7 @@ details, or Python API entries.
 
 cli/index
 api
+detections
 model-config
 training-config
 logging-config

docs/source/tutorials/integrate-with-a-python-pipeline.md

@@ -1,62 +1,50 @@
-# Tutorial: Integrate with a Python pipeline
+# Integrate with a Python pipeline
 
-This tutorial shows a minimal Python workflow for loading audio, running
+This tutorial shows a simple Python workflow for loading audio, running BatDetect2, and inspecting the detections.
-batdetect2, and collecting detections for downstream analysis.
 
-This tutorial is for people who already want to work in Python.
+Use it when you want to work directly in Python rather than through the CLI.
 
-If you mainly want to run the model on recordings,
+If you mainly want to run the model on recordings, start with {doc}`run-inference-on-folder` instead.
-start with {doc}`run-inference-on-folder` instead.
 
 ## Before you start
 
-- BatDetect2 installed in your Python environment.
+You need:
-- A model checkpoint.
-- At least one input audio file.
 
-```{note}
+- BatDetect2 installed in your Python environment,
-This page is more technical than the standard first-run tutorial.
+- at least one input audio file.
-You do not need this page for a normal first use of BatDetect2.
-```
 
-If you are working from this repository checkout, you can start with:
+## What you will do
-
-```text
-src/batdetect2/models/checkpoints/Net2DFast_UK_same.pth.tar
-```
-
-## Outcome
 
 By the end of this tutorial you will have:
 
 - created a `BatDetect2API` object,
 - run inference on one file,
-- inspected the top class, class-score list, and detection score,
+- inspected detections, scores, and features,
-- identified where to go next for feature extraction, saving predictions, and batch workflows.
+- used lower-level audio and spectrogram methods for more control,
+- identified the next API workflows for batch processing, training, fine-tuning, and evaluation.
 
 ## 1. Create the API instance
 
-Load the checkpoint once and reuse the API object for multiple files.
+For a first run, use the built-in default UK model:
 
 ```python
-from pathlib import Path
+from batdetect2 import BatDetect2API
 
-from batdetect2.api_v2 import BatDetect2API
+# If you don't specify a checkpoint the default model will be loaded
-
+api = BatDetect2API.from_checkpoint()
-api = BatDetect2API.from_checkpoint(Path("path/to/model.ckpt"))
 ```
 
+If you want to use a different checkpoint later, see {doc}`../how_to/choose-a-model`.
+
 ## 2. Run inference on one file
 
 `process_file` is the simplest Python entry point when you want one prediction object per recording.
 
 ```python
-from pathlib import Path
+from batdetect2 import BatDetect2API
 
-from batdetect2.api_v2 import BatDetect2API
+api = BatDetect2API.from_checkpoint()
-
+prediction = api.process_file("path/to/audio.wav")
-api = BatDetect2API.from_checkpoint(Path("path/to/model.ckpt"))
-prediction = api.process_file(Path("path/to/audio.wav"))
 
 for detection in prediction.detections:
     top_class = api.get_top_class_name(detection)
@@ -64,21 +52,34 @@ for detection in prediction.detections:
     print(top_class, score)
 ```
 
-`prediction` is a `ClipDetections` object.
+## 3. Understand the prediction objects
 
-It contains:
+`prediction` is a `ClipDetections` object.
+See {doc}`../reference/detections` for the full reference.
+
+Very briefly, `ClipDetections` represents all detections for one processed clip or recording.
+It includes:
 
 - the clip metadata,
-- a list of detections,
+- the list of detections for that clip.
-- a box for each detected event,
-- one detection score per event,
-- a full list of class scores per event,
-- a feature vector per event.
 
-## 3. Inspect class scores, not just the top class
+Each item in `prediction.detections` is a `Detection` object.
 
-If you are exploring results,
+Each `Detection` includes:
-it is often useful to inspect the full ranked class-score list.
+
+- the time-frequency geometry of the event,
+- a detection score,
+- the class scores,
+- a feature vector.
+
+## 4. Inspect detection score and class scores
+
+The detection score and the class scores answer different questions.
+
+- `detection_score` is about whether the model thinks there is a call at that time-frequency location.
+- `class_scores` are about which class the model prefers for that detected event.
+
+So a detection can have a fairly strong detection score, but still have a more uncertain class ranking.
 
 ```python
 for detection in prediction.detections:
@@ -89,30 +90,71 @@ for detection in prediction.detections:
         print(f"  {class_name}: {score:.3f}")
 ```
 
-This helps separate two different questions:
+If you want more detail on class-score inspection, see {doc}`../how_to/inspect-class-scores-in-python`.
 
-- "Did the model think there was a call here?"
+## 5. Inspect the detection features
-- "If there was a call, which class did it score highest?"
 
-## 4. Keep the first workflow small
+Each detection also carries a `features` vector.
 
-Before scaling up, run the API on a few representative files and inspect the results manually.
+These are internal model features attached to the detection.
+They can be useful for things like:
 
-This catches path issues and obviously implausible outputs early.
+- exploratory visualisation,
+- clustering similar detections,
+- comparing detections across files,
+- building downstream analysis pipelines.
 
-## 5. Move to the right next workflow
+They are useful descriptors, but they are not direct ecological labels by themselves.
 
-Once the single-file path is working, choose the next page based on what you need:
+For more detail, see {doc}`../how_to/inspect-detection-features-in-python` and {doc}`../explanation/extracted-features-and-embeddings`.
 
-- save predictions to disk,
+## 6. Use lower-level audio and spectrogram methods for more control
-- inspect class scores more carefully,
-- inspect detection features,
-- process many files in one run.
 
-## What to do next
+If you want finer control over what gets processed and when, the API also lets you work step by step.
 
+For example, you can load the audio yourself, inspect the waveform length, generate the spectrogram, and then run detection on that spectrogram:
+
+```python
+from batdetect2 import BatDetect2API
+
+api = BatDetect2API.from_checkpoint()
+
+audio = api.load_audio("path/to/audio.wav")
+print(audio.shape)
+
+spec = api.generate_spectrogram(audio)
+print(spec.shape)
+
+detections = api.process_spectrogram(spec)
+print(len(detections))
+```
+
+This is helpful when you want to:
+
+- inspect the loaded audio before inference,
+- inspect the generated spectrogram,
+- control which audio segment is processed,
+- run only part of the pipeline in custom code.
+
+You can also call `process_audio(audio)` directly if you already have the waveform array in memory.
+
+## 7. Use the wider API workflows
+
+The Python API is not only for single-file inference.
+It also exposes methods for batch processing, training, evaluation, and fine-tuning.
+
+Examples:
+
+- `process_files(...)` for batch processing from Python,
+- `train(...)` for training,
+- `evaluate(...)` for evaluation,
+- `finetune(...)` for fine-tuning.
+
+Useful next pages:
+
+- Choose a different model: {doc}`../how_to/choose-a-model`
+- Run batch predictions: {doc}`../how_to/run-batch-predictions`
+- Train a custom model: {doc}`train-a-custom-model`
+- Evaluate on a test set: {doc}`evaluate-on-a-test-set`
+- Fine-tune from a checkpoint: {doc}`../how_to/fine-tune-from-a-checkpoint`
 - API reference: {doc}`../reference/api`
-- Inspect ranked class scores: {doc}`../how_to/inspect-class-scores-in-python`
-- Inspect detection features: {doc}`../how_to/inspect-detection-features-in-python`
-- Save predictions to disk: {doc}`../how_to/save-predictions-in-different-output-formats`
-- Learn the CLI happy path: {doc}`run-inference-on-folder`