TraceME Pipeline

TraceME is a video tracking pipeline that runs SAM2 on frame sequences, produces per-frame CSV summaries, and exports annotated videos.

What You Get

• Annotated MP4 outputs per chunk (and a merged MP4).
• Per-frame CSVs per chunk (and a merged CSV).
• A CLI for running the pipeline over frame folders and prompt YAMLs.

Requirements

• Python 3.12+
• SAM2 (installed automatically via pip)
• CUDA GPU recommended for speed (CPU is supported but slow)

Install (PyPI)

pip install traceme-pipeline

Checkpoints (Auto-Download)

TraceME automatically downloads the required SAM2 checkpoint on first run if it is missing. By default, checkpoints are stored in:

~/.cache/traceme/sam2/checkpoints

You can also pre-download all checkpoints:

traceme-download-checkpoints

To change the checkpoint location:

• SAM2_CHECKPOINT_DIR=/path/to/checkpoints

To disable auto-download:

• TRACEME_AUTO_DOWNLOAD=0

Dev Helper (SAM2 + Checkpoints)

If you prefer a local clone of SAM2 (for development), you can still use:

make install

This creates a venv, installs TraceME in editable mode, clones SAM2 into third_party/sam2, and downloads checkpoints.

Configure SAM2 (optional)

If SAM2 lives somewhere else, set:

• SAM2_ROOT=/path/to/sam2 (should contain sam2/ and checkpoints/)
• SAM2_MODEL=tiny|small|base_plus|large|sam3 (default: large)

SAM3 (optional)

The pipeline can also run Meta's SAM3 tracker with the same points/boxes prompt workflow:

pip install 'traceme-pipeline[sam3]'   # requires Python >= 3.12
traceme -i frames/ -o out/ -p prompts.yaml --model sam3

The sam3.pt checkpoint is resolved through the same logic as the SAM2 checkpoints (SAM2_CHECKPOINT, SAM2_CHECKPOINT_DIR, or the default cache dir), but it is not auto-downloaded: it is gated on Hugging Face, so log in with hf auth login, download it from the facebook/sam3 repo, and place it in your checkpoint directory as sam3.pt.

Usage

Run the pipeline:

traceme -i /path/to/frames -o /path/to/output -p /path/to/prompts.yaml

Generate a tasks file for batch runs:

traceme-gen-tasks /path/to/root -o tasks.tsv

Prompt YAML Format

Prompt files must contain a top-level prompts list. See src/traceme/prompts/parser.py for the exact schema and examples.

Outputs

Given frame_dir=/data/frames/clipA, outputs are:

• /output/clipA.csv (merged CSV)
• /output/clipA.mp4 (merged annotated video; one color and id: label per tracked object; exactly one video frame per input frame, so video frame N corresponds to global_frame_idx N)
• /output/clipA_run_summary.json (run status, processed/resumed/failed chunk ids, totals)
• /output/clipA_tmp/ (intermediate chunk files; removed if --del_tmp is set). Chunk folders contain symlinks to the original frames (falling back to copies on filesystems without symlink support), so chunking costs almost no disk space.

CSV columns: chunk_id, global_frame_idx, in_chunk_idx, obj_id, area_px, centroid_x, centroid_y, bbox_x, bbox_y, bbox_w, bbox_h. Frames with no tracked objects produce a single row with an empty obj_id and area_px=0.

Saving Masks (for shape analysis)

Pass --save-masks to persist every object's binary mask, bit-packed, into /output/clipA_masks.npz — one merged archive per video (per-chunk masks are written alongside each chunk's CSV/video during the run, then combined the same way the merged CSV/video are, so --del_tmp does not remove them). Only non-empty masks are stored.

Reload the mask archive:

import numpy as np
from traceme.sam2.io import _unpack_mask

data = np.load("clipA_masks.npz", allow_pickle=True)
for gidx, oid, packed, shp in zip(
    data["global_frame_idx"], data["obj_id"], data["packed"], data["shape"]
):
    mask = _unpack_mask(packed, tuple(shp))  # bool array, shape (H, W)
    # e.g. shape descriptors via skimage:
    # from skimage.measure import regionprops, label
    # props = regionprops(label(mask))[0]
    # props.eccentricity, props.perimeter, props.solidity, ...

Resume & Failures

• Completed chunks are marked in the tmp folder; re-running the same command skips them and continues from the first incomplete chunk. Use --no-resume to reprocess everything.
• If any chunk fails, the pipeline still merges what it has, marks the run "partial" in the run summary, keeps the tmp folder (even with --del_tmp), and exits with code 1. Re-run the same command to retry only the failed chunks.

Troubleshooting

• If SAM2 configs or checkpoints are missing, TraceME will raise a clear error with the expected paths.
• Set HYDRA_FULL_ERROR=1 for detailed SAM2 errors.

License

See LICENSE.