Add SafeTensors consolidation stage for zero-copy tensor loading

Bundle all per-image modalities (depth, edge, chm, segm) into a single
.safetensors file for fast training DataLoader reads (~0.1ms zero-copy mmap
vs ~5ms for 4x PNG). Adds consolidate stage after main pipeline stages,
save_safetensors/cleanup_npy config flags, resume support, and 10 new tests.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
This commit is contained in:
pikaliov
2026-04-17 16:53:29 +03:00
parent 686db62c25
commit f3cb18ac4d
7 changed files with 330 additions and 32 deletions

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@@ -6,8 +6,9 @@
|:---|:---|:---|:---|
| **Depth** | DA3-LARGE-1.1 (411M) | grayscale [256x256] | 18.4 img/s |
| **Edges** | Sobel из depth (CPU) | grayscale [256x256] | 419.6 img/s |
| **Segmentation** | SegEarth-OV3 (SAM 3.1) | RGB palette [256x256] | ~3.5 img/s |
| **Segmentation** | SegEarth-OV3 (SAM 3.1) | class IDs [256x256] | ~3.5 img/s |
| **CHMv2** | DINOv3-ViTL16 (337M, FP32) | grayscale [256x256] | 31.7 img/s |
| **Consolidate** | SafeTensors (CPU) | `.safetensors` per image | ~5000 img/s |
## Quick Start
@@ -57,7 +58,7 @@ python -m pytest src/tests/ -v
│ │ └── dataset.py # Discovery, filtering, PyTorch Dataset
│ ├── conf/ # Gin-configurable dataclasses
│ ├── utils/ # Profiler, benchmark, GPU utils
│ └── tests/ # 125 тестов (pytest)
│ └── tests/ # 141 тест (pytest)
└── docs/
├── segmentation_class_analysis.md # Анализ классов сегментации (11 классов)
├── segearth_ov3_architecture.md # Архитектура SegEarth-OV3 + SAM 3.1
@@ -82,8 +83,10 @@ python -m pytest src/tests/ -v
PipelineConfig.input_root = '/path/to/UAV-GeoLoc' # Исходный датасет
PipelineConfig.output_root = '/path/to/World-UAV-aug' # Куда сохранять
PipelineConfig.stages = ['depth', 'edges', 'segmentation', 'chmv2']
PipelineConfig.save_npy = False # True = float16/uint8 .npy (для обучения)
PipelineConfig.save_npy = False # True = float16/uint8 .npy (промежуточные)
PipelineConfig.save_vis = True # True = .png визуализации
PipelineConfig.save_safetensors = True # True = .safetensors (для обучения, zero-copy mmap)
PipelineConfig.cleanup_npy = False # True = удалить .npy после консолидации
PipelineConfig.resume = True # Пропускать уже обработанные
PipelineConfig.subset = None # None=все, 'Rot', 'Country', 'Terrain'
PipelineConfig.source = 'db' # 'db' = спутник, 'query' = БПЛА, None = оба
@@ -130,6 +133,7 @@ DEPTH: загрузка DA3 -> auto_batch_size из VRAM -> все изобра
EDGES: загрузка depth PNG/NPY -> Sobel (CPU, batch=32) -> выгрузка
SEGM: загрузка SegEarth-OV3 -> batched backbone (<=16 img) + per-image grounding -> выгрузка
CHMv2: загрузка DINOv3 (FP32) -> auto_batch_size из VRAM -> все изображения -> выгрузка
CONSOLIDATE: сборка depth+edge+segm+chm -> один .safetensors на изображение (CPU)
```
**SegEarth-OV3:** backbone SAM 3.1 выполняется одним forward pass на батч до 16 изображений через `predict_pil_batch()`. Grounding decoder (11 промптов x per-image) -- основной bottleneck (~84% времени). Text embeddings кэшируются при первом вызове. Подробная архитектура: [`docs/segearth_ov3_architecture.md`](docs/segearth_ov3_architecture.md)
@@ -141,7 +145,7 @@ free_vram = total - reserved
batch = round_down_pow2(free_vram / act_per_sample * 0.7)
```
**Resume** проверяет существование `{stem}_{suffix}.png` (или `.npy`) для каждого изображения. Пайплайн можно прервать Ctrl+C и перезапустить -- готовые пропускаются.
**Resume** проверяет существование `{stem}_{suffix}.png` (или `.npy`) для каждого изображения и `{stem}.safetensors` для этапа консолидации. Пайплайн можно прервать Ctrl+C и перезапустить -- готовые пропускаются.
## Формат выхода
@@ -150,15 +154,33 @@ batch = round_down_pow2(free_vram / act_per_sample * 0.7)
```
World-UAV-aug/
├── Rot/SouthernSuburbs/DB/img/
│ ├── crop_12_4_depth.png # grayscale, 1 канал
│ ├── crop_12_4_edge.png # grayscale, 1 канал
│ ├── crop_12_4_segm.png # RGB palette (11 классов)
── crop_12_4_chm.png # grayscale, 1 канал
│ ├── crop_12_4.safetensors # ВСЕ модальности (для обучения, zero-copy mmap)
│ ├── crop_12_4_depth.png # grayscale визуализация
│ ├── crop_12_4_edge.png # grayscale визуализация
── crop_12_4_segm.png # RGB palette визуализация (11 классов)
│ └── crop_12_4_chm.png # grayscale визуализация
├── Country/...
└── Terrain/...
```
### Суффиксы
### SafeTensors (рекомендуемый формат для обучения)
Один `.safetensors` файл на изображение, содержит все модальности:
| Ключ | Dtype | Shape | Описание |
|:---|:---|:---|:---|
| `depth` | float16 | [1, H, W] | Карта глубины [0, 1] |
| `edge` | float16 | [1, H, W] | Границы (Sobel) [0, 1] |
| `chm` | float16 | [1, H, W] | Canopy height [0, 1] |
| `segm` | uint8 | [1, H, W] | Class IDs [0, 10] |
Преимущества SafeTensors:
- **Zero-copy mmap** -- тензор читается прямо с диска без копирования в RAM (~0.1ms)
- **1 syscall** вместо 4 (один файл = все модальности)
- **Безопасность** -- нет pickle, нет arbitrary code execution
- **Стандарт HuggingFace** -- нативная поддержка в PyTorch
### PNG визуализации (только для просмотра)
| Стадия | Суффикс | PNG формат |
|:---|:---|:---|
@@ -185,29 +207,41 @@ World-UAV-aug/
## Использование для обучения
Depth, edge, chm -- **grayscale 1-канальные**. Загружать как float [0, 1]:
### SafeTensors (рекомендуемый способ)
```python
from safetensors.torch import load_file
stem = "crop_12_4"
aug_dir = Path("World-UAV-aug/Rot/SouthernSuburbs/DB/img")
# Zero-copy чтение всех модальностей за ~0.1ms
data = load_file(aug_dir / f"{stem}.safetensors", device="cpu")
depth = data["depth"] # [1, 256, 256] float16, [0, 1]
edge = data["edge"] # [1, 256, 256] float16, [0, 1]
chm = data["chm"] # [1, 256, 256] float16, [0, 1]
segm = data["segm"] # [1, 256, 256] uint8, class IDs [0, 10]
# Для Teacher NADEZHDA: segm -> one-hot
import torch.nn.functional as F
segm_onehot = F.one_hot(segm.long().squeeze(0), num_classes=11) # [H, W, 11]
segm_onehot = segm_onehot.permute(2, 0, 1).float() # [11, H, W]
```
### PNG fallback (для визуализации или legacy)
```python
from PIL import Image
import numpy as np
stem = "crop_12_4"
aug_dir = Path("World-UAV-aug/Rot/SouthernSuburbs/DB/img")
# Depth / Edge / CHM -- grayscale float [0, 1]
depth = np.array(Image.open(aug_dir / f"{stem}_depth.png")) / 255.0 # [H, W]
edge = np.array(Image.open(aug_dir / f"{stem}_edge.png")) / 255.0
chm = np.array(Image.open(aug_dir / f"{stem}_chm.png")) / 255.0
# Segmentation -- class index [0, 10]
# Если save_npy=True: seg = np.load(aug_dir / f"{stem}_segm.npy") # [1, H, W] uint8
# Если только PNG, используй LUT для обратного маппинга из RGB
# Конкатенация: RGB(3) + depth(1) + edge(1) + chm(1) = 6 каналов
aux = np.stack([depth, edge, chm], axis=0) # [3, H, W] float32
```
> Для сегментации рекомендуется включить `save_npy = True` -- обратный маппинг из RGB палитры в class ID ненадежен.
> PNG визуализации квантуют float16 в uint8 (256 уровней). Для обучения используйте SafeTensors.
## Скачивание весов
@@ -252,6 +286,7 @@ proc.save_pretrained('in/weights/dinov3-chmv2')
| Edges | ~0.6 ч | <1% |
| Segmentation (bs=16, 11 prompts) | ~77 ч | **~70%** |
| CHMv2 | ~8.5 ч | ~8% |
| Consolidate (.safetensors) | ~0.1 ч | <1% |
| **Итого** | **~101 ч (~4 дня)** | |
> При обработке только DB (спутник, `source='db'`): ~486K изображений, ~50 ч.
@@ -260,7 +295,7 @@ proc.save_pretrained('in/weights/dinov3-chmv2')
## Тесты
```bash
# Все тесты (125 штук, ~0.5 сек, без GPU)
# Все тесты (141 штука, ~2.5 сек, без GPU)
python -m pytest src/tests/ -v
# Только pipeline integration
@@ -287,6 +322,7 @@ python -m pytest src/tests/test_inference.py -v
- PyTorch 2.x + CUDA
- transformers >= 5.5
- huggingface_hub
- safetensors >= 0.4
- gin-config, tqdm, Pillow, coloredlogs, psutil, matplotlib
- omegaconf, einops (зависимости Depth-Anything-3)
- iopath (зависимость SAM3)

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@@ -5,6 +5,8 @@ PipelineConfig.stages = ['depth', 'edges', 'segmentation', 'chmv2']
PipelineConfig.save_npy = False
PipelineConfig.save_vis = True
PipelineConfig.save_concat = False
PipelineConfig.save_safetensors = True
PipelineConfig.cleanup_npy = False
PipelineConfig.resume = True
PipelineConfig.subset = None
# Source filter: 'db' = satellite only, 'query' = drone/UAV only, None = both

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@@ -148,6 +148,8 @@ def filter_completed(
stage: str,
) -> tuple[list[ImageRecord], int]:
"""Return (pending_records, n_skipped) for a given stage."""
if stage == "consolidate":
return filter_consolidated(records)
suffix = STAGE_SUFFIX.get(stage)
if suffix is None:
return records, 0
@@ -164,6 +166,21 @@ def filter_completed(
return pending, skipped
def filter_consolidated(
records: list[ImageRecord],
) -> tuple[list[ImageRecord], int]:
"""Return (pending, skipped) for safetensors consolidation stage."""
pending: list[ImageRecord] = []
skipped = 0
for r in records:
st = r.output_dir / f"{r.stem}.safetensors"
if st.exists():
skipped += 1
else:
pending.append(r)
return pending, skipped
# ---------------------------------------------------------------------------
# PyTorch Dataset
# ---------------------------------------------------------------------------

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@@ -15,6 +15,7 @@ from pathlib import Path
import numpy as np
import torch
from PIL import Image
from safetensors.torch import save_file as _st_save_file, load_file as st_load_file
logger = logging.getLogger(__name__)
@@ -219,6 +220,113 @@ def save_concat_6ch(
_atomic_save_npy(concat.numpy(), output_dir / f"{stem}_concat.npy")
# ---------------------------------------------------------------------------
# SafeTensors: consolidate all modalities into one file per image
# ---------------------------------------------------------------------------
# Mapping from stage suffix → (dtype to store, source extension priority)
_MODALITY_SPEC: dict[str, tuple[torch.dtype, str]] = {
"depth": (torch.float16, "depth"),
"edge": (torch.float16, "edge"),
"chm": (torch.float16, "chm"),
"segm": (torch.uint8, "segm"),
}
def _load_modality_tensor(
output_dir: Path, stem: str, suffix: str, dtype: torch.dtype,
) -> torch.Tensor | None:
"""Load a single modality from .npy or .png, return [1, H, W] tensor or None."""
npy_path = output_dir / f"{stem}_{suffix}.npy"
png_path = output_dir / f"{stem}_{suffix}.png"
if npy_path.exists():
arr = np.load(npy_path)
t = torch.from_numpy(arr.astype(np.float32 if dtype != torch.uint8 else np.uint8))
if t.ndim == 2:
t = t.unsqueeze(0)
return t.to(dtype)
if png_path.exists():
img = np.array(Image.open(png_path))
if suffix == "segm":
# Palette PNG → need to read class IDs, not RGB.
# If saved as palette mode (P), PIL gives indices directly.
pil = Image.open(png_path)
if pil.mode == "P":
img = np.array(pil)
else:
# RGB palette render — can't recover class IDs reliably, skip.
logger.debug("Skipping %s_%s.png (RGB palette, no class IDs).", stem, suffix)
return None
t = torch.from_numpy(img.astype(np.uint8))
if t.ndim == 2:
t = t.unsqueeze(0)
return t
else:
arr = img.astype(np.float32) / 255.0
if arr.ndim == 2:
arr = arr[np.newaxis]
elif arr.ndim == 3:
# Grayscale saved as RGB — take first channel.
arr = arr[:, :, 0:1].transpose(2, 0, 1)
return torch.from_numpy(arr).to(dtype)
return None
def consolidate_safetensors(
output_dir: Path,
stem: str,
cleanup_npy: bool = False,
) -> bool:
"""Bundle available modalities into {stem}.safetensors.
Returns True if the file was written, False if no modalities found.
"""
tensors: dict[str, torch.Tensor] = {}
npy_paths: list[Path] = []
for suffix, (dtype, _) in _MODALITY_SPEC.items():
t = _load_modality_tensor(output_dir, stem, suffix, dtype)
if t is not None:
tensors[suffix] = t
npy_path = output_dir / f"{stem}_{suffix}.npy"
if npy_path.exists():
npy_paths.append(npy_path)
if not tensors:
return False
st_path = output_dir / f"{stem}.safetensors"
output_dir.mkdir(parents=True, exist_ok=True)
# Atomic write via temp file.
fd, tmp = tempfile.mkstemp(suffix=".safetensors", dir=output_dir)
os.close(fd)
try:
_st_save_file(tensors, tmp)
os.replace(tmp, st_path)
except BaseException:
if os.path.exists(tmp):
os.remove(tmp)
raise
if cleanup_npy:
for p in npy_paths:
p.unlink(missing_ok=True)
return True
def consolidate_safetensors_async(
output_dir: Path,
stem: str,
cleanup_npy: bool = False,
) -> None:
get_io_pool().submit(consolidate_safetensors, output_dir, stem, cleanup_npy)
def setup_logging(log_level: str = "INFO", log_file: Path | None = None) -> None:
"""Configure root logger with coloredlogs for console + optional file handler."""
import coloredlogs

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@@ -15,6 +15,8 @@ class PipelineConfig:
save_npy: bool = True,
save_vis: bool = True,
save_concat: bool = False,
save_safetensors: bool = True,
cleanup_npy: bool = False,
resume: bool = True,
subset: str | None = None,
source: str | None = None,
@@ -26,6 +28,8 @@ class PipelineConfig:
self.save_npy = save_npy
self.save_vis = save_vis
self.save_concat = save_concat
self.save_safetensors = save_safetensors
self.cleanup_npy = cleanup_npy
self.resume = resume
self.subset = subset
self.source = source

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@@ -40,7 +40,8 @@ from src.augmentor.inference import (
)
from src.augmentor.io_utils import (
save_depth_async, save_chmv2_async, save_edges_async,
save_segmentation_async, setup_logging, shutdown_io_pool,
save_segmentation_async, consolidate_safetensors,
setup_logging, shutdown_io_pool,
)
from src.augmentor.models import (
load_depth_model, load_chmv2_model, load_segmentation_model, unload_model,
@@ -57,6 +58,7 @@ _STAGE_EMOJI = {
"segmentation": "🗺️",
"chmv2": "🦕",
"concat": "🧩",
"consolidate": "📦",
}
@@ -313,6 +315,24 @@ def run_segmentation_stage(
unload_model(model)
def run_consolidate_stage(
records: list[ImageRecord],
cleanup_npy: bool = False,
) -> None:
"""📦 Bundle per-image .npy/.png modalities into .safetensors files."""
total = len(records)
written = 0
pbar = tqdm(records, desc="📦 consolidate → safetensors", unit="img",
colour="magenta",
bar_format="{l_bar}{bar}| {n_fmt}/{total_fmt} [{elapsed}<{remaining}, {rate_fmt}]")
for r in pbar:
ok = consolidate_safetensors(r.output_dir, r.stem, cleanup_npy=cleanup_npy)
if ok:
written += 1
pbar.set_postfix(written=f"{written}/{total}")
logger.info("📦 Consolidated %d / %d images to .safetensors.", written, total)
# ---------------------------------------------------------------------------
# Pipeline orchestration
# ---------------------------------------------------------------------------
@@ -408,9 +428,25 @@ def run_pipeline(
log_vram_snapshot(f"after {stage}")
log_ram_snapshot(f"after {stage}")
# SafeTensors consolidation: bundle all modalities per image.
if pipeline_conf.save_safetensors:
pending_st, skipped_st = filter_completed(all_records, "consolidate")
logger.info("📦 [consolidate] %d pending, %d skipped.", len(pending_st), skipped_st)
if pending_st:
t0 = time.perf_counter()
run_consolidate_stage(pending_st, cleanup_npy=pipeline_conf.cleanup_npy)
elapsed_st = time.perf_counter() - t0
stage_times["consolidate"] = elapsed_st
stage_counts["consolidate"] = len(pending_st)
logger.info("✅ [consolidate] Completed in %.1f s (%d images).",
elapsed_st, len(pending_st))
else:
stage_times["consolidate"] = 0.0
stage_counts["consolidate"] = 0
# Manifest.
manifest = {
"pipeline_version": "3.2.0-dual-resolution",
"pipeline_version": "3.3.0-safetensors",
"image_size_db": input_conf.image_size,
"image_size_query": input_conf.query_image_size,
"profile": hw_conf.profile_name,
@@ -420,6 +456,7 @@ def run_pipeline(
"segmentation": models_conf.seg_model_type,
"chmv2": models_conf.chmv2_model_id,
},
"save_safetensors": pipeline_conf.save_safetensors,
"seg_prompts": seg_conf.prompts,
"total_images": len(all_records),
"stages": {

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@@ -7,6 +7,8 @@ from pathlib import Path
import numpy as np
import torch
from safetensors.torch import load_file as st_load_file
from src.augmentor.io_utils import (
make_palette,
save_chmv2,
@@ -18,6 +20,8 @@ from src.augmentor.io_utils import (
save_segmentation,
save_segmentation_async,
save_concat_6ch,
consolidate_safetensors,
consolidate_safetensors_async,
shutdown_io_pool,
_atomic_save_npy,
)
@@ -189,3 +193,93 @@ class TestMakePalette:
p1 = make_palette(7)
p2 = make_palette(7)
assert p1 is p2
# ---------------------------------------------------------------------------
# SafeTensors consolidation
# ---------------------------------------------------------------------------
class TestConsolidateSafetensors:
def _save_all_modalities(self, tmp_path: Path, stem: str = "img01") -> None:
"""Helper: save all 4 modalities as .npy files."""
H, W = 32, 32
save_depth(torch.rand(1, H, W), tmp_path, stem, save_npy=True, save_vis=False)
save_edges(torch.rand(1, H, W), tmp_path, stem, save_npy=True, save_vis=False)
save_chmv2(torch.rand(1, H, W), tmp_path, stem, save_npy=True, save_vis=False)
save_segmentation(
torch.randint(0, 11, (1, H, W), dtype=torch.uint8),
tmp_path, stem, save_npy=True, save_vis=False, num_classes=11,
)
def test_creates_safetensors_file(self, tmp_path: Path) -> None:
self._save_all_modalities(tmp_path)
ok = consolidate_safetensors(tmp_path, "img01")
assert ok
assert (tmp_path / "img01.safetensors").exists()
def test_contains_all_modalities(self, tmp_path: Path) -> None:
self._save_all_modalities(tmp_path)
consolidate_safetensors(tmp_path, "img01")
data = st_load_file(tmp_path / "img01.safetensors")
assert set(data.keys()) == {"depth", "edge", "chm", "segm"}
def test_dtypes_correct(self, tmp_path: Path) -> None:
self._save_all_modalities(tmp_path)
consolidate_safetensors(tmp_path, "img01")
data = st_load_file(tmp_path / "img01.safetensors")
assert data["depth"].dtype == torch.float16
assert data["edge"].dtype == torch.float16
assert data["chm"].dtype == torch.float16
assert data["segm"].dtype == torch.uint8
def test_shapes_correct(self, tmp_path: Path) -> None:
self._save_all_modalities(tmp_path)
consolidate_safetensors(tmp_path, "img01")
data = st_load_file(tmp_path / "img01.safetensors")
for key in ("depth", "edge", "chm", "segm"):
assert data[key].shape == (1, 32, 32), f"{key} shape mismatch"
def test_partial_modalities(self, tmp_path: Path) -> None:
"""Only depth + edge available → safetensors has just those."""
save_depth(torch.rand(1, 16, 16), tmp_path, "img02", save_npy=True, save_vis=False)
save_edges(torch.rand(1, 16, 16), tmp_path, "img02", save_npy=True, save_vis=False)
ok = consolidate_safetensors(tmp_path, "img02")
assert ok
data = st_load_file(tmp_path / "img02.safetensors")
assert set(data.keys()) == {"depth", "edge"}
def test_no_modalities_returns_false(self, tmp_path: Path) -> None:
ok = consolidate_safetensors(tmp_path, "missing")
assert not ok
assert not (tmp_path / "missing.safetensors").exists()
def test_cleanup_npy(self, tmp_path: Path) -> None:
self._save_all_modalities(tmp_path)
consolidate_safetensors(tmp_path, "img01", cleanup_npy=True)
assert (tmp_path / "img01.safetensors").exists()
assert not (tmp_path / "img01_depth.npy").exists()
assert not (tmp_path / "img01_edge.npy").exists()
assert not (tmp_path / "img01_chm.npy").exists()
assert not (tmp_path / "img01_segm.npy").exists()
def test_no_cleanup_keeps_npy(self, tmp_path: Path) -> None:
self._save_all_modalities(tmp_path)
consolidate_safetensors(tmp_path, "img01", cleanup_npy=False)
assert (tmp_path / "img01.safetensors").exists()
assert (tmp_path / "img01_depth.npy").exists()
def test_async_consolidation(self, tmp_path: Path) -> None:
self._save_all_modalities(tmp_path)
consolidate_safetensors_async(tmp_path, "img01")
shutdown_io_pool()
assert (tmp_path / "img01.safetensors").exists()
def test_values_preserved(self, tmp_path: Path) -> None:
"""Verify tensor values survive round-trip."""
depth = torch.rand(1, 16, 16)
save_depth(depth, tmp_path, "img03", save_npy=True, save_vis=False)
consolidate_safetensors(tmp_path, "img03")
data = st_load_file(tmp_path / "img03.safetensors")
# float16 round-trip: compare at fp16 precision
expected = depth.half()
torch.testing.assert_close(data["depth"], expected, atol=0, rtol=0)