Refine DRF preprocessing and body-prior pipeline

This commit is contained in:
2026-03-08 04:04:15 +08:00
parent fddbf6eeda
commit bbb41e8dd9
10 changed files with 448 additions and 53 deletions
+5 -5
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@@ -1,6 +1,6 @@
data_cfg:
dataset_name: Scoliosis1K
dataset_root: /mnt/public/data/Scoliosis1K/Scoliosis1K-drf-pkl-118
dataset_root: /mnt/public/data/Scoliosis1K/Scoliosis1K-drf-pkl-118-paper
dataset_partition: ./datasets/Scoliosis1K/Scoliosis1K_118.json
num_workers: 1
remove_no_gallery: false
@@ -10,7 +10,7 @@ evaluator_cfg:
enable_float16: true
restore_ckpt_strict: true
restore_hint: 20000
save_name: DRF
save_name: DRF_paper
eval_func: evaluate_scoliosis
sampler:
batch_shuffle: false
@@ -19,7 +19,7 @@ evaluator_cfg:
frames_all_limit: 720
metric: euc
transform:
- type: BaseSilCuttingTransform
- type: BaseSilTransform
- type: NoOperation
loss_cfg:
@@ -90,7 +90,7 @@ trainer_cfg:
restore_ckpt_strict: true
restore_hint: 0
save_iter: 20000
save_name: DRF
save_name: DRF_paper
sync_BN: true
total_iter: 20000
sampler:
@@ -102,5 +102,5 @@ trainer_cfg:
sample_type: fixed_unordered
type: TripletSampler
transform:
- type: BaseSilCuttingTransform
- type: BaseSilTransform
- type: NoOperation
+106
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@@ -0,0 +1,106 @@
data_cfg:
dataset_name: Scoliosis1K
dataset_root: /mnt/public/data/Scoliosis1K/Scoliosis1K-drf-pkl-118-paper
dataset_partition: ./datasets/Scoliosis1K/Scoliosis1K_118.json
num_workers: 1
remove_no_gallery: false
test_dataset_name: Scoliosis1K
evaluator_cfg:
enable_float16: true
restore_ckpt_strict: true
restore_hint: 20000
save_name: DRF_paper
eval_func: evaluate_scoliosis
sampler:
batch_shuffle: false
batch_size: 1
sample_type: all_ordered
frames_all_limit: 720
metric: euc
transform:
- type: BaseSilTransform
- type: NoOperation
loss_cfg:
- loss_term_weight: 1.0
margin: 0.2
type: TripletLoss
log_prefix: triplet
- loss_term_weight: 1.0
scale: 16
type: CrossEntropyLoss
log_prefix: softmax
log_accuracy: true
model_cfg:
model: DRF
num_pairs: 8
num_metrics: 3
backbone_cfg:
type: ResNet9
block: BasicBlock
in_channel: 2
channels:
- 64
- 128
- 256
- 512
layers:
- 1
- 1
- 1
- 1
strides:
- 1
- 2
- 2
- 1
maxpool: false
SeparateFCs:
in_channels: 512
out_channels: 256
parts_num: 16
SeparateBNNecks:
class_num: 3
in_channels: 256
parts_num: 16
bin_num:
- 16
optimizer_cfg:
lr: 0.1
momentum: 0.9
solver: SGD
weight_decay: 0.0005
scheduler_cfg:
gamma: 0.1
milestones:
- 10000
- 14000
- 18000
scheduler: MultiStepLR
trainer_cfg:
enable_float16: true
fix_BN: false
with_test: false
log_iter: 100
restore_ckpt_strict: true
restore_hint: 0
save_iter: 20000
save_name: DRF_paper
sync_BN: true
total_iter: 20000
sampler:
batch_shuffle: true
batch_size:
- 8
- 8
frames_num_fixed: 30
sample_type: fixed_unordered
type: TripletSampler
transform:
- type: BaseSilTransform
- type: NoOperation
+5 -5
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@@ -1,6 +1,6 @@
data_cfg:
dataset_name: Scoliosis1K
dataset_root: /mnt/public/data/Scoliosis1K/Scoliosis1K-drf-pkl-118
dataset_root: /mnt/public/data/Scoliosis1K/Scoliosis1K-drf-pkl-118-paper
dataset_partition: ./datasets/Scoliosis1K/Scoliosis1K_118.json
num_workers: 1
remove_no_gallery: false
@@ -14,7 +14,7 @@ evaluator_cfg:
enable_float16: true
restore_ckpt_strict: true
restore_hint: 0
save_name: DRF_smoke
save_name: DRF_paper_smoke
eval_func: evaluate_scoliosis
sampler:
batch_shuffle: false
@@ -23,7 +23,7 @@ evaluator_cfg:
frames_all_limit: 720
metric: euc
transform:
- type: BaseSilCuttingTransform
- type: BaseSilTransform
- type: NoOperation
loss_cfg:
@@ -97,7 +97,7 @@ trainer_cfg:
scheduler_reset: false
restore_hint: 0
save_iter: 1
save_name: DRF_smoke
save_name: DRF_paper_smoke
sync_BN: true
total_iter: 1
sampler:
@@ -109,5 +109,5 @@ trainer_cfg:
sample_type: fixed_unordered
type: TripletSampler
transform:
- type: BaseSilCuttingTransform
- type: BaseSilTransform
- type: NoOperation
+26
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@@ -0,0 +1,26 @@
coco18tococo17_args:
transfer_to_coco17: False
padkeypoints_args:
pad_method: knn
use_conf: True
norm_args:
pose_format: coco
use_conf: ${padkeypoints_args.use_conf}
heatmap_image_height: 128
target_body_height: ${norm_args.heatmap_image_height}
heatmap_generator_args:
sigma: 8.0
use_score: ${padkeypoints_args.use_conf}
img_h: ${norm_args.heatmap_image_height}
img_w: ${norm_args.heatmap_image_height}
with_limb: null
with_kp: null
align_args:
align: True
final_img_size: 64
offset: 0
heatmap_image_size: ${norm_args.heatmap_image_height}
+10 -2
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@@ -99,14 +99,22 @@ The PAV pass is implemented from the paper:
4. compute vertical, midline, and angular deviations for the 8 symmetric joint pairs
5. apply IQR filtering per metric
6. average over time
7. min-max normalize across the dataset, or across `TRAIN_SET` when `--stats_partition` is provided
7. min-max normalize across the full dataset (paper default), or across `TRAIN_SET` when `--stats_partition` is provided as an anti-leakage variant
Run:
```bash
uv run python datasets/pretreatment_scoliosis_drf.py \
--pose_data_path=<path_to_pose_pkl> \
--output_path=<path_to_drf_pkl> \
--output_path=<path_to_drf_pkl>
```
To reproduce the paper defaults more closely, the script now uses
`configs/drf/pretreatment_heatmap_drf.yaml` by default, which enables
summed two-channel skeleton maps and a literal 128-pixel height normalization.
If you explicitly want train-only PAV min-max statistics, add:
```bash
--stats_partition=./datasets/Scoliosis1K/Scoliosis1K_118.json
```
+54 -12
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@@ -118,8 +118,8 @@ class GeneratePoseTarget:
ed_x = min(tmp_ed_x + 1, img_w)
st_y = max(tmp_st_y, 0)
ed_y = min(tmp_ed_y + 1, img_h)
x = np.arange(st_x, ed_x, 1, np.float32)
y = np.arange(st_y, ed_y, 1, np.float32)
x = np.arange(st_x, ed_x, dtype=np.float32)
y = np.arange(st_y, ed_y, dtype=np.float32)
# if the keypoint not in the heatmap coordinate system
if not (len(x) and len(y)):
@@ -166,8 +166,8 @@ class GeneratePoseTarget:
min_y = max(tmp_min_y, 0)
max_y = min(tmp_max_y + 1, img_h)
x = np.arange(min_x, max_x, 1, np.float32)
y = np.arange(min_y, max_y, 1, np.float32)
x = np.arange(min_x, max_x, dtype=np.float32)
y = np.arange(min_y, max_y, dtype=np.float32)
if not (len(x) and len(y)):
continue
@@ -324,9 +324,37 @@ class HeatmapToImage:
heatmaps = [cv2.resize(x, (neww, newh)) for x in heatmaps]
return np.ascontiguousarray(np.mean(np.array(heatmaps), axis=-1, keepdims=True).transpose(0,3,1,2))
class HeatmapReducer:
"""Reduce stacked joint/limb heatmaps to a single grayscale channel."""
def __init__(self, reduction: str = "max") -> None:
if reduction not in {"max", "sum"}:
raise ValueError(f"Unsupported heatmap reduction: {reduction}")
self.reduction = reduction
def __call__(self, heatmaps: np.ndarray) -> np.ndarray:
"""
heatmaps: (T, C, H, W)
return: (T, 1, H, W)
"""
if self.reduction == "max":
reduced = np.max(heatmaps, axis=1, keepdims=True)
reduced = np.clip(reduced, 0.0, 1.0)
return (reduced * 255).astype(np.uint8)
reduced = np.sum(heatmaps, axis=1, keepdims=True)
return (reduced * 255.0).astype(np.float32)
class CenterAndScaleNormalizer:
def __init__(self, pose_format="coco", use_conf=True, heatmap_image_height=128) -> None:
def __init__(
self,
pose_format="coco",
use_conf=True,
heatmap_image_height=128,
target_body_height=None,
) -> None:
"""
Parameters:
- pose_format (str): Specifies the format of the keypoints.
@@ -334,10 +362,13 @@ class CenterAndScaleNormalizer:
The supported formats are "coco" or "openpose-x" where 'x' can be either 18 or 25, indicating the number of keypoints used by the OpenPose model.
- use_conf (bool): Indicates whether confidence scores.
- heatmap_image_height (int): Sets the height (in pixels) for the heatmap images that will be normlization.
- target_body_height (float | None): Optional normalized body height. When omitted,
preserve the historical SkeletonGait scaling heuristic.
"""
self.pose_format = pose_format
self.use_conf = use_conf
self.heatmap_image_height = heatmap_image_height
self.target_body_height = target_body_height
def __call__(self, data):
"""
@@ -369,7 +400,13 @@ class CenterAndScaleNormalizer:
# Scale-normalization
y_max = np.max(pose_seq[:, :, 1], axis=-1) # [t]
y_min = np.min(pose_seq[:, :, 1], axis=-1) # [t]
pose_seq *= ((self.heatmap_image_height // 1.5) / (y_max - y_min)[:, np.newaxis, np.newaxis]) # [t, v, 2]
target_body_height = (
float(self.target_body_height)
if self.target_body_height is not None
else float(self.heatmap_image_height // 1.5)
)
body_height = np.maximum(y_max - y_min, 1e-6)
pose_seq *= (target_body_height / body_height)[:, np.newaxis, np.newaxis] # [t, v, 2]
pose_seq += self.heatmap_image_height // 2
@@ -523,16 +560,21 @@ class HeatmapAlignment():
heatmap_imgs: (T, 1, raw_size, raw_size)
return (T, 1, final_img_size, final_img_size)
"""
heatmap_imgs = heatmap_imgs / 255.
heatmap_imgs = np.array([self.center_crop(heatmap_img) for heatmap_img in heatmap_imgs])
return (heatmap_imgs * 255).astype('uint8')
original_dtype = heatmap_imgs.dtype
heatmap_imgs = heatmap_imgs.astype(np.float32) / 255.0
heatmap_imgs = np.array([self.center_crop(heatmap_img) for heatmap_img in heatmap_imgs], dtype=np.float32)
heatmap_imgs = heatmap_imgs * 255.0
if np.issubdtype(original_dtype, np.integer):
return np.clip(heatmap_imgs, 0.0, 255.0).astype(original_dtype)
return heatmap_imgs.astype(original_dtype)
def GenerateHeatmapTransform(
coco18tococo17_args,
padkeypoints_args,
norm_args,
heatmap_generator_args,
align_args
align_args,
reduction="max",
):
base_transform = T.Compose([
@@ -545,7 +587,7 @@ def GenerateHeatmapTransform(
heatmap_generator_args["with_kp"] = False
transform_bone = T.Compose([
GeneratePoseTarget(**heatmap_generator_args),
HeatmapToImage(),
HeatmapReducer(reduction=reduction),
HeatmapAlignment(**align_args)
])
@@ -553,7 +595,7 @@ def GenerateHeatmapTransform(
heatmap_generator_args["with_kp"] = True
transform_joint = T.Compose([
GeneratePoseTarget(**heatmap_generator_args),
HeatmapToImage(),
HeatmapReducer(reduction=reduction),
HeatmapAlignment(**align_args)
])
+10 -4
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@@ -7,7 +7,7 @@ import pickle
import sys
from glob import glob
from pathlib import Path
from typing import Any, TypedDict
from typing import Any, TypedDict, cast
import numpy as np
import yaml
@@ -63,14 +63,17 @@ def get_args() -> argparse.Namespace:
_ = parser.add_argument(
"--heatmap_cfg_path",
type=str,
default="configs/skeletongait/pretreatment_heatmap.yaml",
default="configs/drf/pretreatment_heatmap_drf.yaml",
help="Heatmap preprocessing config used to build the skeleton map branch.",
)
_ = parser.add_argument(
"--stats_partition",
type=str,
default=None,
help="Optional dataset partition JSON. When set, PAV min/max stats use TRAIN_SET ids only.",
help=(
"Optional dataset partition JSON. When set, PAV min/max stats use TRAIN_SET ids only. "
"Omit it to match the paper's dataset-level min-max normalization."
),
)
return parser.parse_args()
@@ -79,7 +82,9 @@ def load_heatmap_cfg(cfg_path: str) -> dict[str, Any]:
with open(cfg_path, "r", encoding="utf-8") as stream:
cfg = yaml.safe_load(stream)
replaced = heatmap_prep.replace_variables(cfg, cfg)
return dict(replaced)
if not isinstance(replaced, dict):
raise TypeError(f"Expected heatmap config dict from {cfg_path}, got {type(replaced).__name__}")
return cast(dict[str, Any], replaced)
def build_pose_transform(cfg: dict[str, Any]) -> T.Compose:
@@ -175,6 +180,7 @@ def main() -> None:
norm_args=heatmap_cfg["norm_args"],
heatmap_generator_args=heatmap_cfg["heatmap_generator_args"],
align_args=heatmap_cfg["align_args"],
reduction="sum",
)
pose_paths = iter_pose_paths(args.pose_data_path)
+82
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@@ -0,0 +1,82 @@
from __future__ import annotations
from typing import Any, Callable, cast
import numpy as np
import torch
from jaxtyping import Float, Int
from .base_model import BaseModel
from opengait.utils.common import list2var, np2var
class BaseModelBody(BaseModel):
"""Base model variant with a separate sequence-level body-prior input."""
def inputs_pretreament(
self,
inputs: tuple[list[np.ndarray], list[int], list[str], list[str], np.ndarray | None],
) -> Any:
seqs_batch, labs_batch, typs_batch, vies_batch, seqL_batch = inputs
seq_trfs = cast(
list[Callable[[Any], Any]],
self.trainer_trfs if self.training else self.evaluator_trfs,
)
if len(seqs_batch) != len(seq_trfs):
raise ValueError(
"The number of types of input data and transform should be same. "
f"But got {len(seqs_batch)} and {len(seq_trfs)}"
)
if len(seqs_batch) < 2:
raise ValueError("BaseModelBody expects one visual input and one body-prior input.")
requires_grad = bool(self.training)
visual_seqs = [
np2var(
np.asarray([trf(fra) for fra in seq]),
requires_grad=requires_grad,
).float()
for trf, seq in zip(seq_trfs[:-1], seqs_batch[:-1])
]
body_trf = seq_trfs[-1]
body_seq = np2var(
np.asarray([body_trf(fra) for fra in seqs_batch[-1]]),
requires_grad=requires_grad,
).float()
labs = list2var(labs_batch).long()
seqL = np2var(seqL_batch).int() if seqL_batch is not None else None
body_features = aggregate_body_features(body_seq, seqL)
if seqL is not None:
seqL_sum = int(seqL.sum().data.cpu().numpy())
ipts = [_[:, :seqL_sum] for _ in visual_seqs]
else:
ipts = visual_seqs
return ipts, labs, typs_batch, vies_batch, seqL, body_features
def aggregate_body_features(
sequence_features: Float[torch.Tensor, "..."],
seqL: Int[torch.Tensor, "1 batch"] | None,
) -> Float[torch.Tensor, "batch pairs metrics"]:
"""Collapse a sampled body-prior sequence back to one vector per sequence."""
if seqL is None:
if sequence_features.ndim < 3:
raise ValueError(f"Expected body prior with >=3 dims, got shape {tuple(sequence_features.shape)}")
return sequence_features.mean(dim=1)
if sequence_features.ndim < 4:
raise ValueError(f"Expected packed body prior with >=4 dims, got shape {tuple(sequence_features.shape)}")
lengths = seqL[0].tolist()
flattened = sequence_features.squeeze(0)
aggregated: list[torch.Tensor] = []
start = 0
for length in lengths:
end = start + int(length)
aggregated.append(flattened[start:end].mean(dim=0))
start = end
return torch.stack(aggregated, dim=0)
+5 -25
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@@ -8,7 +8,7 @@ from jaxtyping import Float, Int
from einops import rearrange
from ..base_model import BaseModel
from ..base_model_body import BaseModelBody
from ..modules import (
HorizontalPoolingPyramid,
PackSequenceWrapper,
@@ -18,7 +18,7 @@ from ..modules import (
)
class DRF(BaseModel):
class DRF(BaseModelBody):
"""Dual Representation Framework from arXiv:2509.00872v1."""
def build_network(self, model_cfg: dict[str, Any]) -> None:
@@ -43,9 +43,10 @@ class DRF(BaseModel):
list[str],
list[str],
Int[torch.Tensor, "1 batch"] | None,
Float[torch.Tensor, "batch pairs metrics"],
],
) -> dict[str, dict[str, Any]]:
ipts, pids, labels, _, seqL = inputs
ipts, pids, labels, _, seqL, key_features = inputs
label_ids = torch.as_tensor(
[LABEL_MAP[str(label).lower()] for label in labels],
device=pids.device,
@@ -58,15 +59,12 @@ class DRF(BaseModel):
else:
heatmaps = rearrange(heatmaps, "n s c h w -> n c s h w")
pav_seq = ipts[1]
pav = aggregate_sequence_features(pav_seq, seqL)
outs = self.Backbone(heatmaps)
outs = self.TP(outs, seqL, options={"dim": 2})[0]
feat = self.HPP(outs)
embed_1 = self.FCs(feat)
embed_1 = self.PGA(embed_1, pav)
embed_1 = self.PGA(embed_1, key_features)
embed_2, logits = self.BNNecks(embed_1)
del embed_2
@@ -120,24 +118,6 @@ class PAVGuidedAttention(nn.Module):
return embeddings * channel_att * spatial_att
def aggregate_sequence_features(
sequence_features: Float[torch.Tensor, "batch seq pairs metrics"],
seqL: Int[torch.Tensor, "1 batch"] | None,
) -> Float[torch.Tensor, "batch pairs metrics"]:
if seqL is None:
return sequence_features.mean(dim=1)
lengths = seqL[0].tolist()
flattened = sequence_features.squeeze(0)
aggregated = []
start = 0
for length in lengths:
end = start + int(length)
aggregated.append(flattened[start:end].mean(dim=0))
start = end
return torch.stack(aggregated, dim=0)
LABEL_MAP: dict[str, int] = {
"negative": 0,
"neutral": 1,
+145
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@@ -0,0 +1,145 @@
from __future__ import annotations
import argparse
import os
import sys
import time
from dataclasses import dataclass
from datetime import datetime
from pathlib import Path
from typing import Final
ERROR_PATTERNS: Final[tuple[str, ...]] = (
"traceback",
"runtimeerror",
"error:",
"exception",
"failed",
"segmentation fault",
"killed",
)
@dataclass(frozen=True)
class JobSpec:
name: str
pid: int
log_path: Path
def parse_args() -> argparse.Namespace:
parser = argparse.ArgumentParser(description="Monitor long-running DRF preprocess/train jobs.")
parser.add_argument("--preprocess-pid", type=int, required=True)
parser.add_argument("--preprocess-log", type=Path, required=True)
parser.add_argument("--launcher-pid", type=int, required=True)
parser.add_argument("--launcher-log", type=Path, required=True)
parser.add_argument("--sentinel-path", type=Path, required=True)
parser.add_argument("--status-log", type=Path, required=True)
parser.add_argument("--poll-seconds", type=float, default=30.0)
return parser.parse_args()
def pid_alive(pid: int) -> bool:
return Path(f"/proc/{pid}").exists()
def read_tail(path: Path, limit: int = 8192) -> str:
if not path.exists():
return ""
with path.open("rb") as handle:
handle.seek(0, os.SEEK_END)
size = handle.tell()
handle.seek(max(size - limit, 0), os.SEEK_SET)
data = handle.read()
return data.decode("utf-8", errors="replace")
def detect_error(log_text: str) -> str | None:
lowered = log_text.lower()
for pattern in ERROR_PATTERNS:
if pattern in lowered:
return pattern
return None
def append_status(path: Path, line: str) -> None:
path.parent.mkdir(parents=True, exist_ok=True)
with path.open("a", encoding="utf-8") as handle:
handle.write(f"{datetime.now().isoformat(timespec='seconds')} {line}\n")
def monitor_job(job: JobSpec, status_log: Path) -> str | None:
tail = read_tail(job.log_path)
error = detect_error(tail)
if error is not None:
append_status(status_log, f"[alert] {job.name}: detected `{error}` in {job.log_path}")
return f"{job.name} log shows `{error}`"
return None
def main() -> int:
args = parse_args()
preprocess = JobSpec("preprocess", args.preprocess_pid, args.preprocess_log)
launcher = JobSpec("launcher", args.launcher_pid, args.launcher_log)
append_status(
args.status_log,
(
"[start] monitoring "
f"preprocess_pid={preprocess.pid} launcher_pid={launcher.pid} "
f"sentinel={args.sentinel_path}"
),
)
preprocess_seen_alive = False
launcher_seen_alive = False
while True:
preprocess_alive = pid_alive(preprocess.pid)
launcher_alive = pid_alive(launcher.pid)
preprocess_seen_alive = preprocess_seen_alive or preprocess_alive
launcher_seen_alive = launcher_seen_alive or launcher_alive
preprocess_error = monitor_job(preprocess, args.status_log)
if preprocess_error is not None:
print(preprocess_error, file=sys.stderr)
return 1
launcher_error = monitor_job(launcher, args.status_log)
if launcher_error is not None:
print(launcher_error, file=sys.stderr)
return 1
sentinel_ready = args.sentinel_path.exists()
append_status(
args.status_log,
(
"[ok] "
f"preprocess_alive={preprocess_alive} "
f"launcher_alive={launcher_alive} "
f"sentinel_ready={sentinel_ready}"
),
)
if preprocess_seen_alive and not preprocess_alive and not sentinel_ready:
append_status(args.status_log, "[alert] preprocess exited before sentinel was written")
print("preprocess exited before sentinel was written", file=sys.stderr)
return 1
launcher_tail = read_tail(launcher.log_path)
train_started = "[start]" in launcher_tail
if launcher_seen_alive and not launcher_alive:
if not train_started and not sentinel_ready:
append_status(args.status_log, "[alert] launcher exited before training started")
print("launcher exited before training started", file=sys.stderr)
return 1
append_status(args.status_log, "[done] launcher exited; monitoring complete")
return 0
time.sleep(args.poll_seconds)
if __name__ == "__main__":
raise SystemExit(main())