README.md

# Spatial Code VSI-Bench Workspace

This workspace evaluates VSI-Bench question answering with several input regimes:
raw video frames, perceived spatial codes from SAM3 + Depth Anything 3 caches,
ground-truth spatial codes from dataset annotations, and a deterministic symbolic
solver. The code is organized so important outputs are reproducible from fixed
inputs, fixed packages, fixed model checkpoints, and fixed SAM3/DA3 caches.

The repository intentionally separates three artifact classes:

- source code and tests in `/workspace`
- data, caches, and model checkpoints under `/root/data` and `/root/models`
- generated results and reports under `/root/results` and `/workspace/reports`

## Quick Start

```bash
# Install packages, clone external repos, download data/models where allowed.
./setup.sh

# Non-interactive setup with a Hugging Face token.
HF_TOKEN=hf_xxx ./setup.sh -y

# Run all unit tests. Tests do not require data, results, or checkpoints.
python -m pytest -q

# Check style and syntax.
python -m black --check /workspace
python -m compileall -q /workspace
```

Useful setup variants:

```bash
./setup.sh --skip-models       # packages + repos + data, but no model checkpoints
./setup.sh --skip-data         # packages + model repos/checkpoints, but no VSI-Bench data
./setup.sh --skip-workspace    # do not sync workspace source from the backup dataset
./setup.sh --with-caches       # also sync cached SAM3/DA3 artifacts from the backup dataset
./setup.sh --with-segvggt      # clone/install optional SegVGGT support
./setup.sh --force             # recreate/re-download targets
```

After setup, use:

```bash
source /root/.venv/bin/activate
source /root/vsi-env.sh
```

`/root/vsi-env.sh` sets the path variables the code expects, including
`VSI_CODES="/root/data/spatial codes"`.

## Runtime Paths

The default paths can be overridden by environment variables, but these are the
expected locations:

| Artifact | Default path | Notes |
|---|---|---|
| Workspace source | `/workspace` | Python packages, tests, setup, README |
| VSI-Bench dataset | `/root/data/VSI-Bench` | `test.jsonl` plus videos under dataset folders |
| Official VSI scorer and meta info | `/root/data/thinking-in-space` | `lmms_eval/tasks/vsibench/utils.py` and `data/meta_info` |
| SAM3/DA3/raw caches | `/root/data/caches` | Input to encoder |
| Spatial codes | `/root/data/spatial codes` | Set with `VSI_CODES`; tests do not depend on it |
| Model repos/checkpoints | `/root/models` | SAM3, DA3, VLM checkpoints, optional SegVGGT |
| Harness results | `/root/results` | One JSON per question |
| Reports | `/workspace/reports` | Generated by `analysis.letters_reports` |

Generated/cache folders in `/workspace` such as `__pycache__`, `.pytest_cache`,
`.cache`, `.ipynb_checkpoints`, `reports`, and `results` are not
source modules. They are not required by tests.

## Reproducibility Contract

Assuming the same inputs, packages, checkpoints, command/config, and frozen
SAM3/DA3 caches:

- spatial-code generation from fixed SAM3/DA3 caches is code-level reproducible
- VLM calls use fixed prompts and deterministic decoding config
- Harness outputs are organized by every meaningful config axis to avoid collisions
- reports have deterministic manifest timestamps by default
- tests use synthetic fixtures and do not require data, results, caches, or checkpoints

Regenerating SAM3/DA3 raw caches themselves is not guaranteed deterministic.

## Workflow Overview

1. Run perception caches if needed with `inference.run` or `inference.launch`.
2. Build perceived spatial codes with `encoder.run` or `encoder.launch`.
3. Run VLM harnesses A-C or symbolic harness F.
4. Regenerate reports with `analysis.letters_reports`.
5. Back up selected outputs with `backup.py`.

## Command Reference

Every CLI supports `--help`; that is the authoritative flag list. The examples below
show the intended interfaces and common combinations.

### Setup And Backup

```bash
./setup.sh [--skip-models] [--skip-data] [--skip-workspace] [--with-caches] [--with-segvggt] [--force]

python backup.py all --repo owner/dataset --dry-run
python backup.py code --repo owner/dataset
python backup.py reports --repo owner/dataset
python backup.py spatial-codes --repo owner/dataset
python backup.py A,B,C --repo owner/dataset
```

`backup.py` targets are defined in `TARGETS`: `code`, `reports`, `spatial-codes`,
Dry-run mode does not import or call `huggingface_hub`.

### Inference: Raw Model Caches

```bash
# One scene, one model backend.
python -m inference.run SCENE --model sam3 --tracking tracking --input uniform --frames 32 --device cuda
python -m inference.run SCENE --model depth-anything-3 --depth metric --input uniform --frames 32 --device cuda

# Batch across selected or all manifest scenes.
python -m inference.launch --model sam3 --tracking tracking --input uniform --frames 32 --scenes scene1,scene2
python -m inference.launch --model depth-anything-3 --depth metric --input uniform --frames 32
```

Important files:

- `inference/__init__.py`: paths, cache path helpers, frame-selection vocabulary
- `inference/adapters.py`: SAM3, DA3, DA3 metric, optional SegVGGT adapters
- `inference/prompts.py`: dataset-specific object prompts for SAM3
- `inference/run.py`: single-scene cache writer
- `inference/launch.py`: multi-scene worker launcher

### Encoder: Spatial Codes

```bash
# One scene from existing SAM3/DA3 caches.
python -m encoder.run SCENE --depth metric --tracking tracking --input uniform --frames 32

# Batch over every manifest scene with required caches.
python -m encoder.launch --depth metric --tracking tracking --input uniform --frames 32

# Full-video mode; depth and tracking remain independently selected.
python -m encoder.run SCENE --depth relative --tracking tracking --video
python -m encoder.launch --depth relative --tracking tracking --video

```

Important files:

- `encoder/config.py`: path construction and validated axes
- `encoder/adapters.py`: raw-cache readers into canonical geometry
- `encoder/geometric.py`: spatial-code construction math
- `encoder/render.py`: writes final explicit spatial-code JSON
- `encoder/run.py`: loads/verifies raw caches and builds one scene
- `encoder/launch.py`: CPU-parallel batch driver

### Experiments: Geometry Hypotheses

```bash
# List available hypothesis forks.
python -m experiments.run --list

# Build one hypothesis spatial code from existing caches only.
python -m experiments.run SCENE --hypothesis "Compute Gravity Before Building Object Instances" --depth metric --tracking tracking --input uniform --frames 64 --format explicit

# Batch all scenes with existing combined or native SAM3/DA3 caches.
python -m experiments.launch --hypothesis "Compute Gravity Before Building Object Instances" --depth metric --tracking tracking --input uniform --frames 64 --format explicit

# Evaluate generated experiment spatial codes with the symbolic scorer.
python -m experiments.evaluate --hypothesis "Compute Gravity Before Building Object Instances" --depth metric --tracking tracking --input uniform --frames 64 --format explicit --quiet --errors
```

Files:

- `experiments/__init__.py`: experiments package marker
- `experiments/README.md`: experiment workflow notes
- `experiments/EXPERIMENT FINDINGS.md`: single consolidated findings report
- `experiments/hypotheses.md`: hypothesis index and notes
- `experiments/config.py`: experiment-local path construction
- `experiments/adapters.py`: build-call adapter for explicit and compact hypothesis forks
- `experiments/loader.py`: dynamic loader for human-readable hypothesis filenames
- `experiments/run.py`: one-scene cache-only hypothesis spatial-code builder
- `experiments/launch.py`: batch launcher over scenes with existing caches
- `experiments/evaluate.py`: symbolic evaluation of experiment spatial codes
- `experiments/hypotheses/*.py`: standalone geometry hypothesis forks; each exposes `build_spatial_code()` and `dump_spatial_code()`

### Symbolic Solver

```bash
# One scene.
python -m symbolic.run SCENE --depth metric --tracking tracking --input uniform --frames 32 --format explicit

# Batch over available spatial codes.
python -m symbolic.launch --depth metric --tracking tracking --input uniform --frames 32 --format explicit

# Interactive/debug solver entry point.
python -m symbolic.solver
```

Important files:

- `symbolic/adapters.py`: adapts compact/explicit codes into solver shape
- `symbolic/solver.py`: deterministic VSI-Bench answering logic
- `symbolic/run.py`: scores one scene and writes per-question JSON
- `symbolic/launch.py`: multi-scene symbolic orchestration

### Harness A: Frames or Native Video

The shared policy is configured in `harness/A/__init__.py` as `QUESTION_PROTOCOLS`. Edit that mapping once to switch either question group. Both groups write to the same configuration folder; each result JSON records its own `question_group` and `protocol`.

```bash
python -m harness.A.run --model qwen3.5-4b --frame-selection uniform --frames 32 --scene SCENE
python -m harness.A.launch --model qwen3.5-4b --frame-selection uniform --frames 32 --scenes scene1,scene2
python -m harness.A.sweep --models all --frame-selections all --frames 16,32
python -m harness.A.run --model qwen3.5-4b --video --scene SCENE
python -m harness.A.launch --model qwen3.5-4b --video
python -m harness.A.sweep --models all --video

```

Question protocols are hardcoded centrally: numerical questions use `base`; multiple-choice questions use `thinking`. `--reasoning-budget` and `--force-budget` affect only thinking questions. Other flags include `--results-dir`, `--rebuild`, `--limit`, `--device`, and `--no-write`.

Files:

- `harness/A/__init__.py`: model paths, protocol constants, result root
- `harness/A/frames.py`: uniform/selective frame sampling
- `harness/A/models.py`: VLM adapters and deterministic generation config
- `harness/A/prompts.py`: VSI-Bench prompt text for frame inputs
- `harness/A/run.py`: one model/config/scene
- `harness/A/launch.py`: persistent GPU workers for one config
- `harness/A/sweep.py`: grid over models, frame selections, frame counts

### Harness B: Spatial Code Text Only

```bash
python -m harness.B.run --model qwen3.5-4b --depth metric --tracking tracking --input-selection uniform --frames 32 --scene SCENE
python -m harness.B.launch --model qwen3.5-4b --depth metric --tracking tracking --input-selection uniform --frames 32
python -m harness.B.sweep --models all --depths metric --trackings tracking --input-selections uniform --frames 32
python -m harness.B.run --model qwen3.5-4b --depth metric --tracking tracking --video --scene SCENE
python -m harness.B.launch --model qwen3.5-4b --depth metric --tracking tracking --video
python -m harness.B.sweep --models all --depths metric --trackings tracking --video
```

Question protocols use the same hardcoded numerical=`base`, multiple-choice=`thinking` policy. Budget flags affect only thinking questions. Other common flags are `--results-dir` and `--rebuild`.

Files:

- `harness/B/__init__.py`: B constants and result root
- `harness/B/spatial_codes.py`: loads perceived explicit JSON
- `harness/B/prompts.py`: spatial-code-only prompt construction
- `harness/B/run.py`: one model/config/scene
- `harness/B/launch.py`: persistent GPU workers for one config
- `harness/B/sweep.py`: grid over model/depth/tracking/input/frame axes

### Harness C: Frames Plus Spatial Code

```bash
python -m harness.C.run --model qwen3.5-4b --depth metric --tracking tracking --input-selection uniform --frames 32 --spatial-code-source frames --spatial-code-input-selection selective --spatial-code-frames 64 --scene SCENE
python -m harness.C.launch --model qwen3.5-4b --depth metric --tracking tracking --input-selection uniform --frames 32 --spatial-code-source frames --spatial-code-input-selection selective --spatial-code-frames 64
python -m harness.C.sweep --models all --depths metric --trackings tracking --input-selections uniform --frames 32 --spatial-code-sources frames --spatial-code-input-selections selective --spatial-code-frames 64
python -m harness.C.run --model qwen3.5-4b --depth metric --tracking tracking --input-selection uniform --frames 32 --spatial-code-source video --scene SCENE
python -m harness.C.launch --model qwen3.5-4b --depth metric --tracking tracking --input-selection uniform --frames 32 --spatial-code-source video
python -m harness.C.sweep --models all --depths metric --trackings tracking --input-selections uniform --frames 32 --spatial-code-sources video
```

Files:

- `harness/C/__init__.py`: C constants and result root
- `harness/C/prompts.py`: combined frames + code prompt construction
- `harness/C/run.py`: one model/config/scene
- `harness/C/launch.py`: persistent GPU workers for one config
- `harness/C/sweep.py`: grid over independent visual-input and spatial-code-input axes

### Harness F: Symbolic Solver As A Harness

```bash
python -m harness.F.run --source perceived --depth metric --tracking tracking --input-selection uniform --frames 32 --scene SCENE
python -m harness.F.launch --source perceived --depth metric --tracking tracking --input-selection uniform --frames 32
python -m harness.F.sweep --sources perceived --depths metric --trackings tracking --input-selections uniform --frames 32
python -m harness.F.run --source perceived --depth metric --tracking tracking --video --scene SCENE
python -m harness.F.launch --source perceived --depth metric --tracking tracking --video
python -m harness.F.sweep --sources perceived --depths metric --trackings tracking --video
```

Files:

- `harness/F/__init__.py`: F constants and result root
- `harness/F/run.py`: symbolic scoring path as a harness
- `harness/F/launch.py`: thin launch entry point to `run.main`
- `harness/F/sweep.py`: grid over symbolic source/config axes

### Analysis And Reports

Current analysis is centered on report generation through `analysis.letters_reports` and
letter-specific wrappers.

```bash
# Regenerate the standard report set from existing results.
python -m analysis.letters_reports \
  --cell A=/root/results/A \
  --cell B=/root/results/B \
  --cell C=/root/results/C \
  --cell D=/root/results/D \
  --cell F=/root/results/F \
  --output-dir /workspace/reports \
  --spatial-codes-dir "/root/data/spatial codes"

# Generate one letter report.
python -m analysis.A_reports --results-dir /root/results/A --output-dir /workspace/reports
python -m analysis.B_reports --results-dir /root/results/B --output-dir /workspace/reports
python -m analysis.C_reports --results-dir /root/results/C --output-dir /workspace/reports
python -m analysis.F_reports --results-dir /root/results/F --output-dir /workspace/reports
```

Files:

- `analysis/letters_reports.py`: shared record discovery, matched summaries, report export
- `analysis/A_reports.py`: wrapper for A report
- `analysis/B_reports.py`: wrapper for B report
- `analysis/C_reports.py`: wrapper for C report
- `analysis/F_reports.py`: wrapper for F report

## Result Layouts

| Producer | Default output layout |
|---|---|
| Inference SAM3 | `/root/data/caches/sam3/<tracking>/frames/<input>/<frames>/<scene>.pt` |
| Inference DA3 | `/root/data/caches/depth-anything-3/<depth>/frames/<input>/<frames>/<scene>.pkl` |
| Encoder combined cache | `/root/data/caches/sam3+depth-anything-3/<tracking>/frames/<input>/<frames>/<scene>.pkl.gz` or `/root/data/caches/sam3+depth-anything-3/<tracking>/video/<scene>.pkl.gz` |
| Perceived spatial code | `$VSI_CODES/sam3+depth-anything-3/<tracking>/frames/<input>/<frames>/explicit/<scene>.json` or `$VSI_CODES/sam3+depth-anything-3/<tracking>/video/explicit/<scene>.json` |
| A results | `/root/results/A/<model>/{<selection>/<frames>|video}/<scene>/<question_id>.json` |
| B results | `/root/results/B/<model>/explicit/<depth>/<tracking>/{<input>/<frames>|video}/<scene>/<question_id>.json` |
| C results | `/root/results/C/<model>/explicit/<depth>/<tracking>/{<input>/<frames>|video}/<scene>/<question_id>.json` |
| F results | `/root/results/F/perceived/<depth>/<tracking>/{<input>/<frames>|video}/explicit/<scene>/<question_id>.json` |
| Reports | `/workspace/reports/*_report.json` |

## Full Source File Index

### Top Level

| File | Purpose |
|---|---|
| `README.md` | This documentation |
| `setup.sh` | Environment, package, data, model, and validation setup |
| `backup.py` | Hugging Face dataset backup utility |
| `.gitattributes` | Git LFS attributes for large/binary artifact patterns |
| `.gitignore` | Excludes generated caches, notebooks, envs, and result folders |
| `selective_frame_counts.csv` | Static frame-count/reference data used by selection workflows |
| `bundles/spatial-codes.tar.gz` | Packed spatial-code artifact used by setup sync |

### `analysis/`

| File | Purpose |
|---|---|
| `analysis/A_reports.py` | CLI wrapper for A report |
| `analysis/B_reports.py` | CLI wrapper for B report |
| `analysis/C_reports.py` | CLI wrapper for C report |
| `analysis/F_reports.py` | CLI wrapper for F report |
| `analysis/letters_reports.py` | Shared analysis/report implementation |

### `encoder/`

| File | Purpose |
|---|---|
| `encoder/__init__.py` | Encoder package marker |
| `encoder/config.py` | Paths and validated dimensions |
| `encoder/adapters.py` | Raw model-cache adapters |
| `encoder/geometric.py` | Spatial-code geometry math |
| `encoder/render.py` | Writes explicit JSON |
| `encoder/run.py` | One-scene perceived-code build |
| `encoder/launch.py` | Batch perceived-code build |

### `harness/`

| File | Purpose |
|---|---|
| `harness/__init__.py` | Harness package marker |
| `harness/A/__init__.py` | A constants/model paths |
| `harness/A/frames.py` | Frame sampling |
| `harness/A/models.py` | VLM adapters |
| `harness/A/prompts.py` | Frame-only prompts |
| `harness/A/run.py` | A one-scene runner |
| `harness/A/launch.py` | A batch launcher |
| `harness/A/sweep.py` | A sweep launcher |
| `harness/B/__init__.py` | B constants |
| `harness/B/spatial_codes.py` | Perceived-code loader |
| `harness/B/prompts.py` | Code-only prompts |
| `harness/B/run.py` | B one-scene runner |
| `harness/B/launch.py` | B batch launcher |
| `harness/B/sweep.py` | B sweep launcher |
| `harness/C/__init__.py` | C constants |
| `harness/C/prompts.py` | Frames+code prompts |
| `harness/C/run.py` | C one-scene runner |
| `harness/C/launch.py` | C batch launcher |
| `harness/C/sweep.py` | C sweep launcher |
| `harness/F/__init__.py` | F constants |
| `harness/F/run.py` | Symbolic solver as harness |
| `harness/F/launch.py` | Thin F launch entry point |
| `harness/F/sweep.py` | F sweep launcher |

### `inference/`

| File | Purpose |
|---|---|
| `inference/__init__.py` | Inference constants/path helpers |
| `inference/adapters.py` | SAM3, DA3, SegVGGT adapters |
| `inference/prompts.py` | Object prompts for SAM3 |
| `inference/run.py` | One-scene raw-cache runner |
| `inference/launch.py` | Batch raw-cache launcher |

### `symbolic/`

| File | Purpose |
|---|---|
| `symbolic/adapters.py` | Code schema adapter for solver |
| `symbolic/solver.py` | Deterministic solver |
| `symbolic/run.py` | One-scene symbolic scoring/writing |
| `symbolic/launch.py` | Batch symbolic scoring |

## Test File Index

The tests mirror source folders. They are written to run without real data, results, or model checkpoints.

### `tests/`

- `tests/__init__.py`
- `tests/conftest.py`

### `tests/test_A/`

- `tests/test_A/__init__.py`
- `tests/test_A/conftest.py`
- `tests/test_A/test_A.py`
- `tests/test_A/test_frames.py`
- `tests/test_A/test_launch.py`
- `tests/test_A/test_models.py`
- `tests/test_A/test_prompts.py`
- `tests/test_A/test_run.py`
- `tests/test_A/test_sweep.py`

### `tests/test_B/`

- `tests/test_B/__init__.py`
- `tests/test_B/conftest.py`
- `tests/test_B/test_B.py`
- `tests/test_B/test_launch.py`
- `tests/test_B/test_prompts.py`
- `tests/test_B/test_run.py`
- `tests/test_B/test_spatial_codes.py`
- `tests/test_B/test_sweep.py`

### `tests/test_C/`

- `tests/test_C/__init__.py`
- `tests/test_C/conftest.py`
- `tests/test_C/test_C.py`
- `tests/test_C/test_launch.py`
- `tests/test_C/test_prompts.py`
- `tests/test_C/test_run.py`
- `tests/test_C/test_sweep.py`

### `tests/test_F/`

- `tests/test_F/__init__.py`
- `tests/test_F/conftest.py`
- `tests/test_F/test_F.py`
- `tests/test_F/test_launch.py`
- `tests/test_F/test_run.py`
- `tests/test_F/test_sweep.py`

### `tests/test_analysis/`

- `tests/test_analysis/__init__.py`
- `tests/test_analysis/conftest.py`
- `tests/test_analysis/test_A_reports.py`
- `tests/test_analysis/test_B_reports.py`
- `tests/test_analysis/test_C_reports.py`
- `tests/test_analysis/test_F_reports.py`
- `tests/test_analysis/test_analysis.py`
- `tests/test_analysis/test_letters_reports.py`

### `tests/`

- `tests/test_backup.py`

### `tests/test_encoder/`

- `tests/test_encoder/conftest.py`
- `tests/test_encoder/test_adapters.py`
- `tests/test_encoder/test_config.py`
- `tests/test_encoder/test_encoder.py`
- `tests/test_encoder/test_geometric.py`
- `tests/test_encoder/test_ground_truth.py`
- `tests/test_encoder/test_init.py`
- `tests/test_encoder/test_launch.py`
- `tests/test_encoder/test_render.py`
- `tests/test_encoder/test_run.py`

### `tests/test_experiments/`

- `tests/test_experiments/__init__.py`
- `tests/test_experiments/conftest.py`
- `tests/test_experiments/test_config.py`
- `tests/test_experiments/test_evaluate.py`
- `tests/test_experiments/test_experiments.py`
- `tests/test_experiments/test_hypotheses.py`
- `tests/test_experiments/test_launch.py`
- `tests/test_experiments/test_loader.py`
- `tests/test_experiments/test_run.py`

### `tests/test_harness/`

- `tests/test_harness/__init__.py`
- `tests/test_harness/conftest.py`
- `tests/test_harness/test_harness.py`

### `tests/test_inference/`

- `tests/test_inference/conftest.py`
- `tests/test_inference/test_adapters.py`
- `tests/test_inference/test_inference.py`
- `tests/test_inference/test_init.py`
- `tests/test_inference/test_launch.py`
- `tests/test_inference/test_prompts.py`
- `tests/test_inference/test_run.py`

### `tests/test_symbolic/`

- `tests/test_symbolic/conftest.py`
- `tests/test_symbolic/test_adapters.py`
- `tests/test_symbolic/test_launch.py`
- `tests/test_symbolic/test_run.py`
- `tests/test_symbolic/test_solver.py`
- `tests/test_symbolic/test_symbolic.py`
## Maintenance Rules

When adding a Python source file, add the corresponding test in the mirrored test
folder. For example:

```text
```

Every `tests/test_<folder>/` directory should contain both `conftest.py` and
`test_<folder>.py`. Tests should use temporary files, monkeypatching, and synthetic
fixtures rather than relying on `/root/data`, `/root/results`, `/workspace/data`, or
model checkpoints.

Before handing off changes, run:

```bash
python -m black /workspace
python -m black --check /workspace
python -m compileall -q /workspace
python -m pytest -q
```