Agile2 agile modeling notebook.

PiperOrigin-RevId: 680052229

chirp/projects/agile2/2_agile_modeling_v2.ipynb

@@ -0,0 +1,314 @@
+{
+  "cells": [
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "id": "AXQAcreKedWU"
+      },
+      "outputs": [],
+      "source": [
+        "#@title Imports. { vertical-output: true }\n",
+        "\n",
+        "import numpy as np\n",
+        "from matplotlib import pyplot as plt\n",
+        "\n",
+        "from chirp.projects.agile2 import audio_loader\n",
+        "from chirp.projects.agile2 import classifier\n",
+        "from chirp.projects.agile2 import classifier_data\n",
+        "from chirp.projects.agile2 import embedding_display\n",
+        "from chirp.projects.hoplite import brutalism\n",
+        "from chirp.projects.hoplite import score_functions\n",
+        "from chirp.projects.hoplite import sqlite_impl\n",
+        "from chirp.projects.zoo import models\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "id": "fz63sWKEedWU"
+      },
+      "outputs": [],
+      "source": [
+        "#@title Load model and connect to database. { vertical-output: true }\n",
+        "\n",
+        "#@markdown Location of database containing audio embeddings.\n",
+        "db_path = ''  #@param {type:'string'}\n",
+        "#@markdown Identifier (eg, name) to attach to labels produced during validation.\n",
+        "annotator_id = 'linnaeus'  #@param {type:'string'}\n",
+        "\n",
+        "db = sqlite_impl.SQLiteGraphSearchDB.create(db_path)\n",
+        "db_model_config = db.get_metadata('model_config')\n",
+        "embed_config = db.get_metadata('embed_config')\n",
+        "model_class = models.model_class_map()[db_model_config.model_key]\n",
+        "embedding_model = model_class.from_config(db_model_config.model_config)\n",
+        "\n",
+        "audio_filepath_loader = audio_loader.make_filepath_loader(\n",
+        "    audio_globs=embed_config.audio_globs,\n",
+        "    window_size_s=embedding_model.window_size_s,\n",
+        "    sample_rate_hz=embedding_model.sample_rate,\n",
+        ")"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {
+        "id": "BVdLJJd9gnjo"
+      },
+      "source": [
+        "# Search"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "id": "7ig3L5dsy3mr"
+      },
+      "outputs": [],
+      "source": [
+        "#@title Load query audio. { vertical-output: true }\n",
+        "\n",
+        "#@markdown The `query_uri` can be a URL, filepath, or Xeno-Canto ID\n",
+        "#@markdown (like `xc777802`, containing an Eastern Whipbird (`easwhi1`)).\n",
+        "query_uri = 'xc777802'  #@param {type:'string'}\n",
+        "query_label = 'easwhi1'  #@param {type:'string'}\n",
+        "\n",
+        "query = embedding_display.QueryDisplay(\n",
+        "    uri=query_uri, offset_s=0.0, window_size_s=5.0, sample_rate_hz=32000)\n",
+        "_ = query.display_interactive()"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "id": "iHUJ_NwQWZNB"
+      },
+      "outputs": [],
+      "source": [
+        "#@title Embed the Query and Search. { vertical-output: true }\n",
+        "\n",
+        "#@markdown Number of results to find and display.\n",
+        "num_results = 50  #@param\n",
+        "query_embedding = embedding_model.embed(\n",
+        "    query.get_audio_window()).embeddings[0, 0]\n",
+        "#@markdown Number of (randomly selected) database entries to search over.\n",
+        "sample_size = 1_000_000  #@param\n",
+        "\n",
+        "#@markdown If checked, search for examples\n",
+        "#@markdown near a particular target score.\n",
+        "target_sampling = False  #@param {type: 'boolean'}\n",
+        "\n",
+        "#@markdown When target sampling, target this score.\n",
+        "target_score = -1.0  #@param\n",
+        "\n",
+        "if not target_sampling:\n",
+        "  target_score = None\n",
+        "score_fn = score_functions.get_score_fn('dot', target_score=target_score)\n",
+        "results, all_scores = brutalism.threaded_brute_search(\n",
+        "    db, query_embedding, num_results, score_fn=score_fn,\n",
+        "    sample_size=sample_size)\n",
+        "\n",
+        "# TODO(tomdenton): Better histogram when target sampling.\n",
+        "_ = plt.hist(all_scores, bins=100)\n",
+        "hit_scores = [r.sort_score for r in results.search_results]\n",
+        "plt.scatter(hit_scores, np.zeros_like(hit_scores), marker='|',\n",
+        "            color='r', alpha=0.5)\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "id": "Y21fWjEwXj68"
+      },
+      "outputs": [],
+      "source": [
+        "#@title Display Results. { vertical-output: true }\n",
+        "\n",
+        "display_results = embedding_display.EmbeddingDisplayGroup.from_search_results(\n",
+        "    results, db, sample_rate_hz=32000, frame_rate=100,\n",
+        "    audio_loader=audio_filepath_loader)\n",
+        "display_results.display(positive_labels=[query_label])"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "id": "G3sIkOqlXzKB"
+      },
+      "outputs": [],
+      "source": [
+        "#@title Save data labels. { vertical-output: true }\n",
+        "\n",
+        "prev_lbls, new_lbls = 0, 0\n",
+        "for lbl in display_results.harvest_labels(annotator_id):\n",
+        "  check = db.insert_label(lbl, skip_duplicates=True)\n",
+        "  new_lbls += check\n",
+        "  prev_lbls += (1 - check)\n",
+        "print('\\nnew_lbls: ', new_lbls)\n",
+        "print('\\nprev_lbls: ', prev_lbls)"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {
+        "id": "o65wpjvyYft-"
+      },
+      "source": [
+        "# Classify"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "id": "qtsJkgcPYg6z"
+      },
+      "outputs": [],
+      "source": [
+        "#@title Classifier training. { vertical-output: true }\n",
+        "\n",
+        "#@markdown Set of labels to classify. If None, auto-populated from the DB.\n",
+        "target_labels = None  #@param\n",
+        "\n",
+        "#@markdown Classifier traning params. These should not require tuning.\n",
+        "learning_rate = 1e-3  #@param\n",
+        "weak_neg_weight = 0.05  #@param\n",
+        "l2_mu = 0.000  #@param\n",
+        "num_steps = 128  #@param\n",
+        "\n",
+        "train_ratio = 0.01  #@param\n",
+        "batch_size = 128  #@param\n",
+        "weak_negatives_batch_size = 128  #@param\n",
+        "loss_fn_name = 'bce'  #@param ['hinge', 'bce']\n",
+        "\n",
+        "data_manager = classifier_data.AgileDataManager(\n",
+        "    target_labels=target_labels,\n",
+        "    db=db,\n",
+        "    train_ratio=0.9,\n",
+        "    min_eval_examples=1,\n",
+        "    batch_size=batch_size,\n",
+        "    weak_negatives_batch_size=weak_negatives_batch_size,\n",
+        "    rng=np.random.default_rng(seed=5))\n",
+        "print('Training for target labels : ')\n",
+        "print(data_manager.get_target_labels())\n",
+        "params, eval_scores = classifier.train_linear_classifier(\n",
+        "    data_manager=data_manager,\n",
+        "    learning_rate=learning_rate,\n",
+        "    weak_neg_weight=weak_neg_weight,\n",
+        "    l2_mu=l2_mu,\n",
+        "    num_train_steps=num_steps,\n",
+        "    loss_name=loss_fn_name,\n",
+        ")\n",
+        "print('\\n' + '-' * 80)\n",
+        "top1 = eval_scores['top1_acc']\n",
+        "print(f'top-1      {top1:.3f}')\n",
+        "rocauc = eval_scores['roc_auc']\n",
+        "print(f'roc_auc    {rocauc:.3f}')\n",
+        "cmap = eval_scores['cmap']\n",
+        "print(f'cmap       {cmap:.3f}')"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "id": "a3N6dzhetkG1"
+      },
+      "outputs": [],
+      "source": [
+        "#@title Review Classifier Results. { vertical-output: true }\n",
+        "\n",
+        "#@markdown Number of results to find and display.\n",
+        "target_label = 'easwhi1'  #@param {type:'string'}\n",
+        "num_results = 50  #@param\n",
+        "\n",
+        "target_label_idx = data_manager.get_target_labels().index(target_label)\n",
+        "class_query = params['beta'][:, target_label_idx]\n",
+        "bias = params['beta_bias'][target_label_idx]\n",
+        "\n",
+        "#@markdown Number of (randomly selected) database entries to search over.\n",
+        "sample_size = 1_000_000  #@param\n",
+        "\n",
+        "#@markdown Whether to use margin-sampling. If checked, search for examples\n",
+        "#@markdown with logits near a particular target score (usually 0).\n",
+        "margin_sampling = False  #@param {type: 'boolean'}\n",
+        "\n",
+        "#@markdown When margin sampling, target this logit.\n",
+        "margin_target_score = -0.0  #@param\n",
+        "if not margin_sampling:\n",
+        "  margin_target_score = None\n",
+        "score_fn = score_functions.get_score_fn(\n",
+        "    'dot', bias=bias, target_score=margin_target_score)\n",
+        "results, all_scores = brutalism.threaded_brute_search(\n",
+        "    db, class_query, num_results, score_fn=score_fn,\n",
+        "    sample_size=sample_size)\n",
+        "\n",
+        "# TODO(tomdenton): Better histogram when margin sampling.\n",
+        "_ = plt.hist(all_scores, bins=100)\n",
+        "hit_scores = [r.sort_score for r in results.search_results]\n",
+        "plt.scatter(hit_scores, np.zeros_like(hit_scores), marker='|',\n",
+        "            color='r', alpha=0.5)\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "id": "EiNoGhyoDF2v"
+      },
+      "outputs": [],
+      "source": [
+        "#@title Display Results. { vertical-output: true }\n",
+        "\n",
+        "display_results = embedding_display.EmbeddingDisplayGroup.from_search_results(\n",
+        "    results, db, sample_rate_hz=32000, frame_rate=100,\n",
+        "    audio_loader=audio_filepath_loader)\n",
+        "display_results.display(positive_labels=[target_label])"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "id": "kEk15jw_B8xL"
+      },
+      "outputs": [],
+      "source": [
+        "#@title Save data labels. { vertical-output: true }\n",
+        "\n",
+        "prev_lbls, new_lbls = 0, 0\n",
+        "for lbl in display_results.harvest_labels(annotator_id):\n",
+        "  check = db.insert_label(lbl, skip_duplicates=True)\n",
+        "  new_lbls += check\n",
+        "  prev_lbls += (1 - check)\n",
+        "print('\\nnew_lbls: ', new_lbls)\n",
+        "print('\\nprev_lbls: ', prev_lbls)"
+      ]
+    }
+  ],
+  "metadata": {
+    "colab": {
+      "last_runtime": {
+        "build_target": "",
+        "kind": "local"
+      },
+      "private_outputs": true,
+      "provenance": [],
+      "toc_visible": true
+    },
+    "kernelspec": {
+      "display_name": "Python 3",
+      "name": "python3"
+    },
+    "language_info": {
+      "name": "python"
+    }
+  },
+  "nbformat": 4,
+  "nbformat_minor": 0
+}

chirp/projects/agile2/audio_loader.py

@@ -0,0 +1,69 @@
+# coding=utf-8
+# Copyright 2024 The Perch Authors.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Audio loader function helpers."""
+
+import os
+from typing import Callable
+
+from chirp import audio_utils
+from etils import epath
+import numpy as np
+
+
+def make_filepath_loader(
+    audio_globs: dict[str, tuple[str, str]],
+    sample_rate_hz: int = 32000,
+    window_size_s: float = 5.0,
+    dtype: str = 'float32',
+) -> Callable[[str, float], np.ndarray]:
+  """Create a function for loading audio from a source ID and offset.
+
+  Note that if multiple globs match a given source ID, the first match is used.
+
+  Args:
+    audio_globs: Mapping from dataset name to pairs of `(root directory, file
+      glob)`. (See `embed.EmbedConfig` for details.)
+    sample_rate_hz: Sample rate of the audio.
+    window_size_s: Window size of the audio.
+    dtype: Data type of the audio.
+
+  Returns:
+    Function for loading audio from a source ID and offset.
+
+  Raises:
+    ValueError if no audio path is found for the given source ID.
+  """
+
+  def loader(source_id: str, offset_s: float) -> np.ndarray:
+    found_path = None
+    for base_path, _ in audio_globs.values():
+      path = epath.Path(base_path) / source_id
+      if path.exists():
+        found_path = path
+        break
+    if found_path is None:
+      raise ValueError('No audio path found for source_id: ', source_id)
+    return np.array(
+        audio_utils.load_audio_window(
+            found_path.as_posix(),
+            offset_s,
+            sample_rate=sample_rate_hz,
+            window_size_s=window_size_s,
+        ),
+        dtype=dtype,
+    )
+
+  return loader

chirp/projects/agile2/classifier.py

@@ -124,7 +124,7 @@ def train_linear_classifier(
   """Train a linear classifier."""
   optimizer = optax.adam(learning_rate=learning_rate)
   embedding_dim = data_manager.db.embedding_dimension()
-  num_classes = len(data_manager.target_labels)
+  num_classes = len(data_manager.get_target_labels())
   params = {
       'beta': jnp.zeros((embedding_dim, num_classes)),
       'beta_bias': jnp.zeros((num_classes,)),