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- accelerometer/juvExpBP01/BP_2021-08-09_10-11-42_504687_0720000_14812.wav +3 -0
- calibrations/.gitattributes +35 -0
- calibrations/README.md +38 -0
- calibrations/reference_points.csv +52 -0
- explore.ipynb +396 -0
- metadata.json +78 -0
- split_summary.json +44 -0
README.md
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| 1 |
+
---
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| 2 |
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license: cc-by-4.0
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pretty_name: V33DA
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task_categories:
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- audio-classification
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- video-classification
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tags:
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- animal-behavior
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- bioacoustics
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- bird-vocalization
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- multimodal
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- 3d-pose
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- localization
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- attribution
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- radio-telemetry
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- accelerometer
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size_categories:
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- 10K<n<100K
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configs:
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- config_name: default
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data_files:
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- split: train
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path: v33da-*.parquet
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---
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# V33DA: Benchmarking Vocal Attribution in Freely-Behaving Zebra Finches
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V33DA is a multimodal benchmark for vocal attribution and 3D vocal localization in small groups of freely behaving zebra finches recorded in the BirdPark aviary. Each released sample is a single vocalization event with synchronized microphone audio, video, 3D pose, radio telemetry, and the accelerometer-derived on-body verification signal used to establish the ground-truth caller label.
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The dataset is designed so that caller labels do not reduce to the same room-acoustic attribution problem solved by the benchmark models. Instead, the release follows the paper’s extraction pipeline: candidate events are proposed from the body-mounted verification channel, manually reviewed, and then filtered by geometric and motion consistency before inclusion.
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## Paper Summary
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Recordings were collected from groups of 3--4 zebra finches during natural social interactions. The sensing setup aligns the same event across:
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- five cage microphones sampled at 24,414 Hz
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- three synchronized camera views
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- five 3D body keypoints per bird
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- 21 per-bird radio telemetry signals per frame
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- the raw accelerometer-derived vibration signal carried by each bird
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The benchmark supports a task introduced in the paper:
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1. vocal attribution: identify which visible bird produced the vocalization
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## Modalities
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Each parquet row corresponds to one released vocalization event and includes:
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- `audio_path`: relative path to the multichannel cage-microphone WAV
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- `accelerometer_path`: relative path to the multichannel accelerometer WAV
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- `video_path`: relative path to the aligned composite MP4 clip
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- `keypoints_3d`: triangulated 3D body pose
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| 54 |
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- `keypoints_2d_top`: 2D keypoints in the top-view image space
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- `keypoints_2d_back`: 2D keypoints in the back-view image space
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- `radio_*`: synchronized per-bird radio telemetry arrays
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| 57 |
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- `bird_color`: color identity used as the source of truth for caller assignment
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- `vocalizer_idx`: index of the vocalizing bird
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Media is stored as external files and referenced from parquet by path.
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## Labeling and Filtering
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The paper’s released set is built from a reviewed candidate pool. After manual verification, samples are retained only if they satisfy the release filters:
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- overlapping vocalizations removed
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- 3D-to-2D reprojection error `<= 40 px`
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| 68 |
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- maximum frame-to-frame 2D displacement `<= 40 px`
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- no NaNs in released 3D or 2D keypoints
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Color is the source of truth for the released vocalizer identity.
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## Release Contents
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| 74 |
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This standalone release contains:
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- `v33da-*.parquet`: pooled parquet shards for the full release
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| 78 |
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- `audio/`: multichannel microphone WAV files
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- `accelerometer/`: multichannel accelerometer WAV files
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- `clips/`: aligned composite MP4 clips
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- `calibrations/`: per-experiment camera calibration files
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- `explore.ipynb`: notebook for dataset exploration and reprojection
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- `metadata.json`: release schema and filter metadata
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## Dataset Size
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- released samples: `33,625`
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- pooled parquet shards: `23`
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- experiments: `3`
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- individuals: `11`
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Per-group counts in this standalone release:
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- `juvExpBP01 / blue`: `5,735`
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- `juvExpBP01 / peach`: `2,277`
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- `juvExpBP01 / red`: `3,963`
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- `juvExpBP01 / white`: `4,244`
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- `juvExpBP02 / blue`: `4,923`
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- `juvExpBP02 / peach`: `4,589`
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- `juvExpBP02 / red`: `2,065`
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- `juvExpBP05 / brown`: `3,633`
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- `juvExpBP05 / purple`: `2,140`
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- `juvExpBP05 / yellow`: `56`
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## Using the Dataset
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The canonical release format is the pooled `v33da-*.parquet` set. Each binary array column is serialized with `numpy.save`, so decoding is:
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```python
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import io
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import numpy as np
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arr = np.load(io.BytesIO(raw_bytes))
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```
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The included `explore.ipynb` notebook shows how to:
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- load parquet shards
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- inspect audio, accelerometer, video, pose, and radio
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- use the shipped camera calibrations to reproject 3D keypoints into 2D views
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## Limitations
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As discussed in the paper, V33DA is collected in one aviary with one recording geometry across three experiments. Cross-experiment evaluation therefore combines bird-identity shift, group-composition shift, and recording-date shift. The released benchmark also excludes overlapping vocalizations and filters out samples with poor geometric consistency or excessive motion.
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## Citation
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If you use this dataset, please cite the accompanying paper:
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```bibtex
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@inproceedings{basha2026v33da,
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| 132 |
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title={V33DA: Benchmarking Vocal Attribution in Freely-Behaving Zebra Finches},
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author={Basha, Maris and Wang, Yuhang and Chen, Xiaoran and Cheng, Longbiao and Yapura, Luca and Salzmann, Mathieu and Hahnloser, Richard},
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| 134 |
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booktitle={XXX},
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| 135 |
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year={2026}
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}
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```
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accelerometer/juvExpBP01/BP_2021-07-31_06-21-00_336025_0060000_1418.wav
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calibrations/.gitattributes
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|
|
|
|
| 1 |
+
---
|
| 2 |
+
license: mit
|
| 3 |
+
tags:
|
| 4 |
+
- zebra-finch
|
| 5 |
+
- camera-calibration
|
| 6 |
+
- birdpark
|
| 7 |
+
---
|
| 8 |
+
|
| 9 |
+
# BirdPark Camera Calibration & Metadata
|
| 10 |
+
|
| 11 |
+
Camera intrinsics, extrinsics, and bird-color metadata for the BirdPark multi-view tracking setup (3 cameras: top, back, side).
|
| 12 |
+
|
| 13 |
+
## Download
|
| 14 |
+
|
| 15 |
+
```bash
|
| 16 |
+
pip install huggingface_hub
|
| 17 |
+
```
|
| 18 |
+
|
| 19 |
+
```python
|
| 20 |
+
from huggingface_hub import snapshot_download
|
| 21 |
+
snapshot_download("songbirdini/birdpark_calibration", local_dir="tracking/data")
|
| 22 |
+
```
|
| 23 |
+
|
| 24 |
+
Or from the TCBI analysis project:
|
| 25 |
+
|
| 26 |
+
```bash
|
| 27 |
+
python -m tracking.download_calibration
|
| 28 |
+
```
|
| 29 |
+
|
| 30 |
+
## Contents
|
| 31 |
+
|
| 32 |
+
| File | Description |
|
| 33 |
+
|------|-------------|
|
| 34 |
+
| `calibration_{view}.npz` | Camera intrinsic matrix (K) + distortion coefficients |
|
| 35 |
+
| `camera_pose_{view}.pkl` | Camera extrinsic rotation (rvec) + translation (tvec) |
|
| 36 |
+
| `metadata.csv` | Experiment -> bird ID -> backpack color mapping |
|
| 37 |
+
|
| 38 |
+
Views: `top` (1292x1292), `back` (2202x724), `side` (774x1292, rotated 90 degrees)
|
calibrations/reference_points.csv
ADDED
|
@@ -0,0 +1,52 @@
|
|
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|
|
| 1 |
+
Unnamed: 0,X(mm),Y(mm),Z(mm),Index,position
|
| 2 |
+
116.0,323.8442214,665.019271042,1081.815583062,1,wedge_wall
|
| 3 |
+
116.0,348.072516622,665.019271042,1081.815583062,2,wedge_wall
|
| 4 |
+
116.0,323.8442214,665.019271042,1106.043878284,3,wedge_wall
|
| 5 |
+
116.0,348.072516622,665.019271042,1106.043878284,4,wedge_wall
|
| 6 |
+
116.0,318.072516622,640.019271042,1106.043878284,5,wedge_wall
|
| 7 |
+
116.0,348.072516622,640.019271042,1106.043878284,6,wedge_wall
|
| 8 |
+
116.0,348.072516622,640.019271042,1076.043878284,7,wedge_wall
|
| 9 |
+
116.0,1041.351578025,665.019271042,1425.482844503,8,wedege_door
|
| 10 |
+
116.0,1017.123282803,665.019271042,1449.711139724,9,wedege_door
|
| 11 |
+
116.0,1041.351578025,665.019271042,1449.711139724,10,wedege_door
|
| 12 |
+
116.0,1017.123282803,640.019271042,1425.482844503,11,wedege_door
|
| 13 |
+
116.0,1047.123282803,640.019271042,1425.482844503,12,wedege_door
|
| 14 |
+
116.0,1017.123282803,640.019271042,1455.482844503,13,wedege_door
|
| 15 |
+
116.0,1046.816821976,511.40242249,1046.34693913,14,nest_wall
|
| 16 |
+
116.0,1046.816821976,511.40242249,1076.34693913,15,nest_wall
|
| 17 |
+
116.0,1046.816821976,511.40242249,1142.444265892,16,nest_wall
|
| 18 |
+
116.0,1046.816821976,511.40242249,1172.444265892,17,nest_wall
|
| 19 |
+
116.0,1076.816821976,511.40242249,1172.444265892,18,nest_wall
|
| 20 |
+
116.0,1046.866821976,536.40242249,1172.89693913,19,nest_wall
|
| 21 |
+
116.0,1046.866821976,633.40242249,1174.562380619,20,nest_wall
|
| 22 |
+
116.0,323.619270346,664.044900977,1454.04025791,21,nest_door
|
| 23 |
+
116.0,418.374120452,664.044900977,1449.93949076,22,nest_door
|
| 24 |
+
116.0,288.378977449,511.40242249,1455.179783657,23,nest_door
|
| 25 |
+
116.0,318.378977449,511.40242249,1455.179783657,24,nest_door
|
| 26 |
+
116.0,318.378977449,536.40242249,1455.179783657,25,nest_door
|
| 27 |
+
116.0,414.928977449,536.40242249,1455.229783657,26,nest_door
|
| 28 |
+
116.0,384.474745717,511.40242249,1455.179783657,27,nest_door
|
| 29 |
+
116.0,414.474745717,511.40242249,1455.179783657,28,nest_door
|
| 30 |
+
116.0,414.474745717,511.40242249,1485.179783657,29,nest_door
|
| 31 |
+
116.0,241.599015305,253.988072442,999.741100871,30,plate_left
|
| 32 |
+
116.0,678.599014328,255.488072442,999.770322483,31,plate_left
|
| 33 |
+
116.0,241.563441168,255.488072442,1531.741099682,32,plate_left
|
| 34 |
+
116.0,678.56344019,253.988072442,1531.770321294,33,plate_left
|
| 35 |
+
116.0,686.40473411,255.488072442,999.770407744,34,plate_right
|
| 36 |
+
116.0,1123.40473411,255.488072442,999.770407744,35,plate_right
|
| 37 |
+
116.0,686.40473411,255.488072442,1531.770407744,36,plate_right
|
| 38 |
+
116.0,1123.40473411,255.488072442,1531.770407744,37,plate_right
|
| 39 |
+
116.0,1017.123282803,665.019271042,1425.482844503,38,wedege_door
|
| 40 |
+
116.0,-90.761717388,1529.988072442,667.932180663,A,box
|
| 41 |
+
116.0,-90.761717388,1529.988072442,1563.932180663,D,box
|
| 42 |
+
116.0,-90.761717388,235.988072442,1563.932180663,C,box
|
| 43 |
+
116.0,-90.761717388,235.988072442,667.932180663,B,box
|
| 44 |
+
116.0,1155.238282612,1529.988072442,667.932180663,E,box
|
| 45 |
+
116.0,1155.238282612,1529.988072442,1563.932180663,H,box
|
| 46 |
+
116.0,1155.238282612,235.988072442,667.932180663,F,box
|
| 47 |
+
116.0,1155.238282612,235.988072442,1563.932180663,G,box
|
| 48 |
+
,855.0,1265.0,1266.0,,Mic1(roughly)
|
| 49 |
+
,1020.0,775.0,1266.0,,Mic2-right
|
| 50 |
+
,303.0,775.0,1266.0,,Mic3-left
|
| 51 |
+
,682.0,775.0,1060.0,,Mic4-back
|
| 52 |
+
,682.0,775.0,1434.0,,Mic5-door
|
explore.ipynb
ADDED
|
@@ -0,0 +1,396 @@
|
|
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|
|
|
| 1 |
+
{
|
| 2 |
+
"cells": [
|
| 3 |
+
{
|
| 4 |
+
"cell_type": "markdown",
|
| 5 |
+
"metadata": {},
|
| 6 |
+
"source": [
|
| 7 |
+
"# v33da Dataset Explorer\n",
|
| 8 |
+
"\n",
|
| 9 |
+
"Standalone exploration notebook for `v33da`.\n",
|
| 10 |
+
"\n",
|
| 11 |
+
"This notebook mirrors the old `v33dl` dataset explorer style, but targets the standalone `v33da` package directly. It walks through:\n",
|
| 12 |
+
"\n",
|
| 13 |
+
"1. Loading pooled parquet shards\n",
|
| 14 |
+
"2. Picking a sample\n",
|
| 15 |
+
"3. Audio and accelerometer signals\n",
|
| 16 |
+
"4. Video clips\n",
|
| 17 |
+
"5. 3D pose and 2D keypoints\n",
|
| 18 |
+
"6. Camera calibration and reprojection\n",
|
| 19 |
+
"7. Radio telemetry"
|
| 20 |
+
]
|
| 21 |
+
},
|
| 22 |
+
{
|
| 23 |
+
"cell_type": "markdown",
|
| 24 |
+
"metadata": {},
|
| 25 |
+
"source": [
|
| 26 |
+
"## 0. Setup\n",
|
| 27 |
+
"\n",
|
| 28 |
+
"If you already have the standalone dataset locally, just run the next cell. The notebook resolves the dataset root automatically."
|
| 29 |
+
]
|
| 30 |
+
},
|
| 31 |
+
{
|
| 32 |
+
"cell_type": "code",
|
| 33 |
+
"execution_count": null,
|
| 34 |
+
"metadata": {},
|
| 35 |
+
"outputs": [],
|
| 36 |
+
"source": [
|
| 37 |
+
"from __future__ import annotations\n",
|
| 38 |
+
"\n",
|
| 39 |
+
"import io\n",
|
| 40 |
+
"import pickle\n",
|
| 41 |
+
"from pathlib import Path\n",
|
| 42 |
+
"\n",
|
| 43 |
+
"import cv2\n",
|
| 44 |
+
"import matplotlib.pyplot as plt\n",
|
| 45 |
+
"import numpy as np\n",
|
| 46 |
+
"import pyarrow.parquet as pq\n",
|
| 47 |
+
"import soundfile as sf\n",
|
| 48 |
+
"\n",
|
| 49 |
+
"R_ZUP = np.array([[1, 0, 0], [0, 0, -1], [0, 1, 0]], dtype=np.float64)\n",
|
| 50 |
+
"KEYPOINT_NAMES = [\"beak\", \"head\", \"backpack\", \"tailbe\", \"tailend\"]\n",
|
| 51 |
+
"RADIO_KEYS = [\n",
|
| 52 |
+
" \"frq\", \"thetaS\", \"thetaA\", \"thetaB\", \"thetaC\", \"thetaD\",\n",
|
| 53 |
+
" \"phiA\", \"phiB\", \"phiC\", \"phiD\", \"phiM\",\n",
|
| 54 |
+
" \"powRA\", \"powRB\", \"powRC\", \"powRD\", \"powRM\",\n",
|
| 55 |
+
" \"powNA\", \"powNB\", \"powNC\", \"powND\", \"powNM\",\n",
|
| 56 |
+
"]\n",
|
| 57 |
+
"\n",
|
| 58 |
+
"def resolve_dataset_root() -> Path:\n",
|
| 59 |
+
" cwd = Path.cwd()\n",
|
| 60 |
+
" if (cwd / 'metadata.json').exists() and (cwd / 'audio').exists():\n",
|
| 61 |
+
" return cwd\n",
|
| 62 |
+
" candidate = Path('/home/songbird/code/v33da/data/v33da')\n",
|
| 63 |
+
" if candidate.exists():\n",
|
| 64 |
+
" return candidate\n",
|
| 65 |
+
" raise FileNotFoundError('Could not locate the standalone v33da dataset root.')\n",
|
| 66 |
+
"\n",
|
| 67 |
+
"DATASET_ROOT = resolve_dataset_root()\n",
|
| 68 |
+
"DATASET_ROOT"
|
| 69 |
+
]
|
| 70 |
+
},
|
| 71 |
+
{
|
| 72 |
+
"cell_type": "markdown",
|
| 73 |
+
"metadata": {},
|
| 74 |
+
"source": [
|
| 75 |
+
"## 1. Load & Inspect the Pooled Parquet Shards"
|
| 76 |
+
]
|
| 77 |
+
},
|
| 78 |
+
{
|
| 79 |
+
"cell_type": "code",
|
| 80 |
+
"execution_count": null,
|
| 81 |
+
"metadata": {},
|
| 82 |
+
"outputs": [],
|
| 83 |
+
"source": [
|
| 84 |
+
"pooled_shards = sorted(DATASET_ROOT.glob('v33da-*.parquet'))\n",
|
| 85 |
+
"len(pooled_shards), pooled_shards[:3]"
|
| 86 |
+
]
|
| 87 |
+
},
|
| 88 |
+
{
|
| 89 |
+
"cell_type": "code",
|
| 90 |
+
"execution_count": null,
|
| 91 |
+
"metadata": {},
|
| 92 |
+
"outputs": [],
|
| 93 |
+
"source": [
|
| 94 |
+
"first_table = pq.read_table(pooled_shards[0])\n",
|
| 95 |
+
"first_table.schema"
|
| 96 |
+
]
|
| 97 |
+
},
|
| 98 |
+
{
|
| 99 |
+
"cell_type": "markdown",
|
| 100 |
+
"metadata": {},
|
| 101 |
+
"source": [
|
| 102 |
+
"## 2. Pick a Sample"
|
| 103 |
+
]
|
| 104 |
+
},
|
| 105 |
+
{
|
| 106 |
+
"cell_type": "code",
|
| 107 |
+
"execution_count": null,
|
| 108 |
+
"metadata": {},
|
| 109 |
+
"outputs": [],
|
| 110 |
+
"source": [
|
| 111 |
+
"def decode_array(blob: bytes) -> np.ndarray:\n",
|
| 112 |
+
" return np.load(io.BytesIO(blob))\n",
|
| 113 |
+
"\n",
|
| 114 |
+
"def resolve_media_path(path_str: str) -> Path:\n",
|
| 115 |
+
" path = Path(path_str)\n",
|
| 116 |
+
" if path.is_absolute():\n",
|
| 117 |
+
" return path\n",
|
| 118 |
+
" return DATASET_ROOT / path\n",
|
| 119 |
+
"\n",
|
| 120 |
+
"def load_sample(shard_index: int = 0, row_index: int = 0):\n",
|
| 121 |
+
" row = pq.read_table(pooled_shards[shard_index]).slice(row_index, 1).to_pylist()[0]\n",
|
| 122 |
+
" row['keypoints_3d'] = decode_array(row['keypoints_3d'])\n",
|
| 123 |
+
" row['keypoints_2d_top'] = decode_array(row['keypoints_2d_top'])\n",
|
| 124 |
+
" row['keypoints_2d_back'] = decode_array(row['keypoints_2d_back'])\n",
|
| 125 |
+
" radio = {}\n",
|
| 126 |
+
" for key in RADIO_KEYS:\n",
|
| 127 |
+
" radio[key] = decode_array(row[f'radio_{key}'])\n",
|
| 128 |
+
" row['radio'] = radio\n",
|
| 129 |
+
" row['audio_file'] = resolve_media_path(row['audio_path'])\n",
|
| 130 |
+
" row['accelerometer_file'] = resolve_media_path(row['accelerometer_path'])\n",
|
| 131 |
+
" row['video_file'] = resolve_media_path(row['video_path'])\n",
|
| 132 |
+
" return row\n",
|
| 133 |
+
"\n",
|
| 134 |
+
"sample = load_sample(shard_index=0, row_index=0)\n",
|
| 135 |
+
"sample['id'], sample['experiment'], sample['bird_color'], sample['video_file'].name"
|
| 136 |
+
]
|
| 137 |
+
},
|
| 138 |
+
{
|
| 139 |
+
"cell_type": "markdown",
|
| 140 |
+
"metadata": {},
|
| 141 |
+
"source": [
|
| 142 |
+
"## 3. Audio and Accelerometer"
|
| 143 |
+
]
|
| 144 |
+
},
|
| 145 |
+
{
|
| 146 |
+
"cell_type": "code",
|
| 147 |
+
"execution_count": null,
|
| 148 |
+
"metadata": {},
|
| 149 |
+
"outputs": [],
|
| 150 |
+
"source": [
|
| 151 |
+
"audio, sr_audio = sf.read(sample['audio_file'])\n",
|
| 152 |
+
"accel, sr_accel = sf.read(sample['accelerometer_file'])\n",
|
| 153 |
+
"audio.shape, sr_audio, accel.shape, sr_accel"
|
| 154 |
+
]
|
| 155 |
+
},
|
| 156 |
+
{
|
| 157 |
+
"cell_type": "code",
|
| 158 |
+
"execution_count": null,
|
| 159 |
+
"metadata": {},
|
| 160 |
+
"outputs": [],
|
| 161 |
+
"source": [
|
| 162 |
+
"fig, axes = plt.subplots(2, 1, figsize=(14, 6), sharex=False)\n",
|
| 163 |
+
"axes[0].plot(audio)\n",
|
| 164 |
+
"axes[0].set_title('Microphone audio (all channels)')\n",
|
| 165 |
+
"axes[1].plot(accel)\n",
|
| 166 |
+
"axes[1].set_title('Accelerometer audio (all channels)')\n",
|
| 167 |
+
"plt.tight_layout()"
|
| 168 |
+
]
|
| 169 |
+
},
|
| 170 |
+
{
|
| 171 |
+
"cell_type": "markdown",
|
| 172 |
+
"metadata": {},
|
| 173 |
+
"source": [
|
| 174 |
+
"## 4. Video"
|
| 175 |
+
]
|
| 176 |
+
},
|
| 177 |
+
{
|
| 178 |
+
"cell_type": "code",
|
| 179 |
+
"execution_count": null,
|
| 180 |
+
"metadata": {},
|
| 181 |
+
"outputs": [],
|
| 182 |
+
"source": [
|
| 183 |
+
"cap = cv2.VideoCapture(str(sample['video_file']))\n",
|
| 184 |
+
"ok, frame_bgr = cap.read()\n",
|
| 185 |
+
"cap.release()\n",
|
| 186 |
+
"frame = cv2.cvtColor(frame_bgr, cv2.COLOR_BGR2RGB) if ok else None\n",
|
| 187 |
+
"frame.shape if frame is not None else None"
|
| 188 |
+
]
|
| 189 |
+
},
|
| 190 |
+
{
|
| 191 |
+
"cell_type": "code",
|
| 192 |
+
"execution_count": null,
|
| 193 |
+
"metadata": {},
|
| 194 |
+
"outputs": [],
|
| 195 |
+
"source": [
|
| 196 |
+
"plt.figure(figsize=(12, 8))\n",
|
| 197 |
+
"plt.imshow(frame)\n",
|
| 198 |
+
"plt.title(sample['video_file'].name)\n",
|
| 199 |
+
"plt.axis('off')"
|
| 200 |
+
]
|
| 201 |
+
},
|
| 202 |
+
{
|
| 203 |
+
"cell_type": "markdown",
|
| 204 |
+
"metadata": {},
|
| 205 |
+
"source": [
|
| 206 |
+
"## 5. 3D Pose and 2D Keypoints"
|
| 207 |
+
]
|
| 208 |
+
},
|
| 209 |
+
{
|
| 210 |
+
"cell_type": "code",
|
| 211 |
+
"execution_count": null,
|
| 212 |
+
"metadata": {},
|
| 213 |
+
"outputs": [],
|
| 214 |
+
"source": [
|
| 215 |
+
"kp3d = sample['keypoints_3d']\n",
|
| 216 |
+
"kp2d_top = sample['keypoints_2d_top']\n",
|
| 217 |
+
"kp2d_back = sample['keypoints_2d_back']\n",
|
| 218 |
+
"kp3d.shape, kp2d_top.shape, kp2d_back.shape"
|
| 219 |
+
]
|
| 220 |
+
},
|
| 221 |
+
{
|
| 222 |
+
"cell_type": "code",
|
| 223 |
+
"execution_count": null,
|
| 224 |
+
"metadata": {},
|
| 225 |
+
"outputs": [],
|
| 226 |
+
"source": [
|
| 227 |
+
"mid = kp3d.shape[0] // 2\n",
|
| 228 |
+
"mid_beaks = kp3d[mid, :, 0]\n",
|
| 229 |
+
"\n",
|
| 230 |
+
"fig = plt.figure(figsize=(7, 6))\n",
|
| 231 |
+
"ax = fig.add_subplot(111, projection='3d')\n",
|
| 232 |
+
"ax.scatter(mid_beaks[:, 0], mid_beaks[:, 1], mid_beaks[:, 2], s=60)\n",
|
| 233 |
+
"for bird_idx, pt in enumerate(mid_beaks):\n",
|
| 234 |
+
" ax.text(pt[0], pt[1], pt[2], str(bird_idx))\n",
|
| 235 |
+
"ax.set_xlabel('X (mm)')\n",
|
| 236 |
+
"ax.set_ylabel('Y (mm)')\n",
|
| 237 |
+
"ax.set_zlabel('Z (mm)')\n",
|
| 238 |
+
"ax.set_title('Mid-frame beak positions')"
|
| 239 |
+
]
|
| 240 |
+
},
|
| 241 |
+
{
|
| 242 |
+
"cell_type": "markdown",
|
| 243 |
+
"metadata": {},
|
| 244 |
+
"source": [
|
| 245 |
+
"## 6. Camera Calibration and Reprojection"
|
| 246 |
+
]
|
| 247 |
+
},
|
| 248 |
+
{
|
| 249 |
+
"cell_type": "code",
|
| 250 |
+
"execution_count": null,
|
| 251 |
+
"metadata": {},
|
| 252 |
+
"outputs": [],
|
| 253 |
+
"source": [
|
| 254 |
+
"def load_calibration(experiment: str, view: str):\n",
|
| 255 |
+
" exp_dir = DATASET_ROOT / 'calibrations' / experiment\n",
|
| 256 |
+
" npz = np.load(exp_dir / f'calibration_{view}.npz')\n",
|
| 257 |
+
" with open(exp_dir / f'camera_pose_{view}.pkl', 'rb') as handle:\n",
|
| 258 |
+
" pose = pickle.load(handle)\n",
|
| 259 |
+
" return {\n",
|
| 260 |
+
" 'K': npz['mtx'],\n",
|
| 261 |
+
" 'dist': npz['dist'],\n",
|
| 262 |
+
" 'rvec': pose['rvec'],\n",
|
| 263 |
+
" 'tvec': pose['tvec'],\n",
|
| 264 |
+
" }\n",
|
| 265 |
+
"\n",
|
| 266 |
+
"def project_zup(points_xyz_mm: np.ndarray, calibration: dict) -> np.ndarray:\n",
|
| 267 |
+
" pts = np.asarray(points_xyz_mm, dtype=np.float64)\n",
|
| 268 |
+
" pts_cam = (R_ZUP @ pts.T).T\n",
|
| 269 |
+
" proj, _ = cv2.projectPoints(pts_cam, calibration['rvec'], calibration['tvec'], calibration['K'], calibration['dist'])\n",
|
| 270 |
+
" return proj.reshape(-1, 2)\n",
|
| 271 |
+
"\n",
|
| 272 |
+
"def reproject_view(row, view: str):\n",
|
| 273 |
+
" cal = load_calibration(row['experiment'], view)\n",
|
| 274 |
+
" kp3d_mid = row['keypoints_3d'][mid]\n",
|
| 275 |
+
" kp2d_mid = row[f'keypoints_2d_{view}'][mid]\n",
|
| 276 |
+
" projected = np.full_like(kp2d_mid, np.nan, dtype=np.float64)\n",
|
| 277 |
+
" errors = np.full(kp2d_mid.shape[:2], np.nan, dtype=np.float64)\n",
|
| 278 |
+
" for bird_idx in range(kp3d_mid.shape[0]):\n",
|
| 279 |
+
" valid3d = ~np.any(np.isnan(kp3d_mid[bird_idx]), axis=1)\n",
|
| 280 |
+
" valid2d = ~np.any(np.isnan(kp2d_mid[bird_idx]), axis=1)\n",
|
| 281 |
+
" if valid3d.any():\n",
|
| 282 |
+
" projected[bird_idx, valid3d] = project_zup(kp3d_mid[bird_idx, valid3d], cal)\n",
|
| 283 |
+
" valid = valid2d & valid3d\n",
|
| 284 |
+
" if valid.any():\n",
|
| 285 |
+
" errors[bird_idx, valid] = np.linalg.norm(projected[bird_idx, valid] - kp2d_mid[bird_idx, valid], axis=1)\n",
|
| 286 |
+
" return kp2d_mid, projected, errors\n",
|
| 287 |
+
"\n",
|
| 288 |
+
"top_obs, top_proj, top_err = reproject_view(sample, 'top')\n",
|
| 289 |
+
"back_obs, back_proj, back_err = reproject_view(sample, 'back')\n",
|
| 290 |
+
"np.nanmedian(top_err), np.nanmedian(back_err)"
|
| 291 |
+
]
|
| 292 |
+
},
|
| 293 |
+
{
|
| 294 |
+
"cell_type": "code",
|
| 295 |
+
"execution_count": null,
|
| 296 |
+
"metadata": {},
|
| 297 |
+
"outputs": [],
|
| 298 |
+
"source": [
|
| 299 |
+
"def plot_reprojection(ax, observed, projected, title):\n",
|
| 300 |
+
" colors = ['tab:red', 'tab:orange', 'tab:blue', 'tab:green']\n",
|
| 301 |
+
" for bird_idx in range(observed.shape[0]):\n",
|
| 302 |
+
" obs = observed[bird_idx]\n",
|
| 303 |
+
" proj = projected[bird_idx]\n",
|
| 304 |
+
" valid_obs = ~np.any(np.isnan(obs), axis=1)\n",
|
| 305 |
+
" valid_proj = ~np.any(np.isnan(proj), axis=1)\n",
|
| 306 |
+
" if valid_obs.any():\n",
|
| 307 |
+
" ax.scatter(obs[valid_obs, 0], obs[valid_obs, 1], c=colors[bird_idx % len(colors)], marker='o', alpha=0.8)\n",
|
| 308 |
+
" if valid_proj.any():\n",
|
| 309 |
+
" ax.scatter(proj[valid_proj, 0], proj[valid_proj, 1], c=colors[bird_idx % len(colors)], marker='x', alpha=0.8)\n",
|
| 310 |
+
" valid = valid_obs & valid_proj\n",
|
| 311 |
+
" for kp_idx in np.where(valid)[0]:\n",
|
| 312 |
+
" ax.plot([obs[kp_idx, 0], proj[kp_idx, 0]], [obs[kp_idx, 1], proj[kp_idx, 1]], color=colors[bird_idx % len(colors)], alpha=0.35)\n",
|
| 313 |
+
" ax.set_title(title)\n",
|
| 314 |
+
" ax.invert_yaxis()\n",
|
| 315 |
+
" ax.set_aspect('equal')\n",
|
| 316 |
+
" ax.grid(alpha=0.2)\n",
|
| 317 |
+
"\n",
|
| 318 |
+
"fig, axes = plt.subplots(1, 2, figsize=(14, 6))\n",
|
| 319 |
+
"plot_reprojection(axes[0], top_obs, top_proj, f'top | median reproj = {np.nanmedian(top_err):.2f}px')\n",
|
| 320 |
+
"plot_reprojection(axes[1], back_obs, back_proj, f'back | median reproj = {np.nanmedian(back_err):.2f}px')\n",
|
| 321 |
+
"plt.tight_layout()"
|
| 322 |
+
]
|
| 323 |
+
},
|
| 324 |
+
{
|
| 325 |
+
"cell_type": "markdown",
|
| 326 |
+
"metadata": {},
|
| 327 |
+
"source": [
|
| 328 |
+
"## 7. Radio Telemetry"
|
| 329 |
+
]
|
| 330 |
+
},
|
| 331 |
+
{
|
| 332 |
+
"cell_type": "code",
|
| 333 |
+
"execution_count": null,
|
| 334 |
+
"metadata": {},
|
| 335 |
+
"outputs": [],
|
| 336 |
+
"source": [
|
| 337 |
+
"sample['radio']['powRA'].shape, sample['radio']['thetaS'].shape"
|
| 338 |
+
]
|
| 339 |
+
},
|
| 340 |
+
{
|
| 341 |
+
"cell_type": "code",
|
| 342 |
+
"execution_count": null,
|
| 343 |
+
"metadata": {},
|
| 344 |
+
"outputs": [],
|
| 345 |
+
"source": [
|
| 346 |
+
"fig, axes = plt.subplots(2, 1, figsize=(14, 6), sharex=True)\n",
|
| 347 |
+
"axes[0].plot(sample['radio']['powRA'].T)\n",
|
| 348 |
+
"axes[0].set_title('radio powRA per bird')\n",
|
| 349 |
+
"axes[1].plot(sample['radio']['thetaS'].T)\n",
|
| 350 |
+
"axes[1].set_title('radio thetaS per bird')\n",
|
| 351 |
+
"plt.tight_layout()"
|
| 352 |
+
]
|
| 353 |
+
},
|
| 354 |
+
{
|
| 355 |
+
"cell_type": "markdown",
|
| 356 |
+
"metadata": {},
|
| 357 |
+
"source": [
|
| 358 |
+
"## 8. Iterate Efficiently\n",
|
| 359 |
+
"\n",
|
| 360 |
+
"Use this pattern if you want to scan pooled shards without loading everything into RAM."
|
| 361 |
+
]
|
| 362 |
+
},
|
| 363 |
+
{
|
| 364 |
+
"cell_type": "code",
|
| 365 |
+
"execution_count": null,
|
| 366 |
+
"metadata": {},
|
| 367 |
+
"outputs": [],
|
| 368 |
+
"source": [
|
| 369 |
+
"for shard in pooled_shards[:2]:\n",
|
| 370 |
+
" table = pq.read_table(shard, columns=['experiment', 'bird_color'])\n",
|
| 371 |
+
" print(shard.name, table.num_rows)"
|
| 372 |
+
]
|
| 373 |
+
}
|
| 374 |
+
],
|
| 375 |
+
"metadata": {
|
| 376 |
+
"kernelspec": {
|
| 377 |
+
"display_name": "Python 3",
|
| 378 |
+
"language": "python",
|
| 379 |
+
"name": "python3"
|
| 380 |
+
},
|
| 381 |
+
"language_info": {
|
| 382 |
+
"codemirror_mode": {
|
| 383 |
+
"name": "ipython",
|
| 384 |
+
"version": 3
|
| 385 |
+
},
|
| 386 |
+
"file_extension": ".py",
|
| 387 |
+
"mimetype": "text/x-python",
|
| 388 |
+
"name": "python",
|
| 389 |
+
"nbconvert_exporter": "python",
|
| 390 |
+
"pygments_lexer": "ipython3",
|
| 391 |
+
"version": "3.12"
|
| 392 |
+
}
|
| 393 |
+
},
|
| 394 |
+
"nbformat": 4,
|
| 395 |
+
"nbformat_minor": 5
|
| 396 |
+
}
|
metadata.json
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
| 1 |
+
{
|
| 2 |
+
"dataset_name": "v33da",
|
| 3 |
+
"per_bird_limit": null,
|
| 4 |
+
"num_rows": 33625,
|
| 5 |
+
"groups": {
|
| 6 |
+
"juvExpBP01/blue": 5735,
|
| 7 |
+
"juvExpBP01/peach": 2277,
|
| 8 |
+
"juvExpBP01/red": 3963,
|
| 9 |
+
"juvExpBP01/white": 4244,
|
| 10 |
+
"juvExpBP02/blue": 4923,
|
| 11 |
+
"juvExpBP02/peach": 4589,
|
| 12 |
+
"juvExpBP02/red": 2065,
|
| 13 |
+
"juvExpBP05/brown": 3633,
|
| 14 |
+
"juvExpBP05/purple": 2140,
|
| 15 |
+
"juvExpBP05/yellow": 56
|
| 16 |
+
},
|
| 17 |
+
"schema": [
|
| 18 |
+
"id",
|
| 19 |
+
"experiment",
|
| 20 |
+
"date",
|
| 21 |
+
"video_stem",
|
| 22 |
+
"bird_name",
|
| 23 |
+
"bird_color",
|
| 24 |
+
"vocalizer_idx",
|
| 25 |
+
"n_frames",
|
| 26 |
+
"keypoints_3d",
|
| 27 |
+
"keypoints_2d_top",
|
| 28 |
+
"keypoints_2d_back",
|
| 29 |
+
"audio",
|
| 30 |
+
"audio_path",
|
| 31 |
+
"accelerometer",
|
| 32 |
+
"accelerometer_path",
|
| 33 |
+
"video_path",
|
| 34 |
+
"radio_frq",
|
| 35 |
+
"radio_thetaS",
|
| 36 |
+
"radio_thetaA",
|
| 37 |
+
"radio_thetaB",
|
| 38 |
+
"radio_thetaC",
|
| 39 |
+
"radio_thetaD",
|
| 40 |
+
"radio_phiA",
|
| 41 |
+
"radio_phiB",
|
| 42 |
+
"radio_phiC",
|
| 43 |
+
"radio_phiD",
|
| 44 |
+
"radio_phiM",
|
| 45 |
+
"radio_powRA",
|
| 46 |
+
"radio_powRB",
|
| 47 |
+
"radio_powRC",
|
| 48 |
+
"radio_powRD",
|
| 49 |
+
"radio_powRM",
|
| 50 |
+
"radio_powNA",
|
| 51 |
+
"radio_powNB",
|
| 52 |
+
"radio_powNC",
|
| 53 |
+
"radio_powND",
|
| 54 |
+
"radio_powNM"
|
| 55 |
+
],
|
| 56 |
+
"filters": {
|
| 57 |
+
"max_reproj_error_px": 40.0,
|
| 58 |
+
"max_global_displacement_px": null,
|
| 59 |
+
"max_intra_frame_displacement_px": 40.0,
|
| 60 |
+
"motion_filter_mode": "frame_to_frame_only",
|
| 61 |
+
"nan_policy": "drop_rows_with_any_nan_in_3d_or_2d",
|
| 62 |
+
"overlap_pad_sec": 0.01
|
| 63 |
+
},
|
| 64 |
+
"overlap_removed_before_build": 3784,
|
| 65 |
+
"frames": {
|
| 66 |
+
"description": "Full composite video chunks aligned to each vocalization window",
|
| 67 |
+
"format": "MP4 (mp4v codec)",
|
| 68 |
+
"frame_rate_hz": 47.6837158203125,
|
| 69 |
+
"pad_frames": 1
|
| 70 |
+
},
|
| 71 |
+
"external_media": {
|
| 72 |
+
"audio_rows_with_paths": 33625,
|
| 73 |
+
"accelerometer_rows_with_paths": 33625,
|
| 74 |
+
"video_rows_with_paths": 33625,
|
| 75 |
+
"media_jobs_path": "media_jobs.jsonl",
|
| 76 |
+
"media_results_path": "media_results.jsonl"
|
| 77 |
+
}
|
| 78 |
+
}
|
split_summary.json
ADDED
|
@@ -0,0 +1,44 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"dataset_root": "/home/songbird/code/v33da/data/v33da",
|
| 3 |
+
"total_rows": 33625,
|
| 4 |
+
"session_split_counts": {
|
| 5 |
+
"test": 7391,
|
| 6 |
+
"train": 19365,
|
| 7 |
+
"val": 6869
|
| 8 |
+
},
|
| 9 |
+
"generalization_split_counts": {
|
| 10 |
+
"test": 5829,
|
| 11 |
+
"train": 21491,
|
| 12 |
+
"val": 6305
|
| 13 |
+
},
|
| 14 |
+
"session_by_experiment": {
|
| 15 |
+
"train": {
|
| 16 |
+
"juvExpBP01": 12881,
|
| 17 |
+
"juvExpBP02": 4455,
|
| 18 |
+
"juvExpBP05": 2029
|
| 19 |
+
},
|
| 20 |
+
"val": {
|
| 21 |
+
"juvExpBP01": 1008,
|
| 22 |
+
"juvExpBP02": 4155,
|
| 23 |
+
"juvExpBP05": 1706
|
| 24 |
+
},
|
| 25 |
+
"test": {
|
| 26 |
+
"juvExpBP01": 2330,
|
| 27 |
+
"juvExpBP02": 2967,
|
| 28 |
+
"juvExpBP05": 2094
|
| 29 |
+
}
|
| 30 |
+
},
|
| 31 |
+
"generalization_by_experiment": {
|
| 32 |
+
"train": {
|
| 33 |
+
"juvExpBP01": 12881,
|
| 34 |
+
"juvExpBP02": 8610
|
| 35 |
+
},
|
| 36 |
+
"val": {
|
| 37 |
+
"juvExpBP01": 3338,
|
| 38 |
+
"juvExpBP02": 2967
|
| 39 |
+
},
|
| 40 |
+
"test": {
|
| 41 |
+
"juvExpBP05": 5829
|
| 42 |
+
}
|
| 43 |
+
}
|
| 44 |
+
}
|