Spaces:
Running
Running
File size: 48,703 Bytes
d323f56 085a6f7 094b1a4 c421c59 b45d525 d323f56 085a6f7 a02c8c4 085a6f7 d323f56 ff7f2b3 bf0aa04 2baa1e7 085a6f7 befc6dd 085a6f7 094b1a4 a02c8c4 094b1a4 963dd1a 094b1a4 085a6f7 d323f56 094b1a4 a02c8c4 094b1a4 a02c8c4 094b1a4 d323f56 a02c8c4 d323f56 094b1a4 d323f56 094b1a4 d323f56 094b1a4 d323f56 094b1a4 d323f56 094b1a4 d323f56 094b1a4 a02c8c4 befc6dd a02c8c4 befc6dd a02c8c4 befc6dd a02c8c4 befc6dd a02c8c4 befc6dd a02c8c4 befc6dd a02c8c4 befc6dd 5091532 befc6dd a02c8c4 befc6dd 5091532 befc6dd 5091532 befc6dd a02c8c4 befc6dd 085a6f7 befc6dd 085a6f7 a02c8c4 befc6dd a02c8c4 085a6f7 a02c8c4 befc6dd a02c8c4 befc6dd a02c8c4 befc6dd 085a6f7 befc6dd 085a6f7 094b1a4 befc6dd a02c8c4 93d7a1f a02c8c4 93d7a1f 1e7d078 094b1a4 085a6f7 094b1a4 085a6f7 094b1a4 a02c8c4 094b1a4 befc6dd 085a6f7 befc6dd 094b1a4 085a6f7 094b1a4 085a6f7 094b1a4 085a6f7 094b1a4 085a6f7 094b1a4 085a6f7 094b1a4 085a6f7 094b1a4 085a6f7 094b1a4 085a6f7 094b1a4 085a6f7 094b1a4 085a6f7 094b1a4 085a6f7 094b1a4 085a6f7 094b1a4 085a6f7 094b1a4 085a6f7 c609645 a02c8c4 c609645 085a6f7 c609645 085a6f7 c609645 085a6f7 c609645 085a6f7 c609645 085a6f7 befc6dd 085a6f7 c609645 085a6f7 c609645 085a6f7 c609645 085a6f7 c609645 085a6f7 c609645 085a6f7 c609645 085a6f7 c609645 085a6f7 c609645 085a6f7 c609645 085a6f7 befc6dd 085a6f7 c609645 085a6f7 c609645 085a6f7 c609645 085a6f7 c609645 085a6f7 c609645 085a6f7 b45d525 094b1a4 d323f56 085a6f7 d323f56 085a6f7 c609645 d323f56 085a6f7 d323f56 a02c8c4 085a6f7 d323f56 085a6f7 5b2e7ae 085a6f7 c609645 085a6f7 c609645 085a6f7 c609645 085a6f7 c609645 085a6f7 d323f56 085a6f7 d323f56 085a6f7 d323f56 085a6f7 c609645 085a6f7 d323f56 085a6f7 d323f56 085a6f7 c609645 085a6f7 d323f56 085a6f7 d323f56 b45d525 085a6f7 094b1a4 862d7cb d323f56 a02c8c4 befc6dd a02c8c4 d323f56 befc6dd d323f56 befc6dd d323f56 085a6f7 befc6dd d323f56 085a6f7 befc6dd d323f56 befc6dd d323f56 befc6dd d323f56 085a6f7 d323f56 befc6dd d323f56 085a6f7 befc6dd d323f56 085a6f7 d323f56 a02c8c4 d323f56 862d7cb d323f56 ca79af9 d323f56 085a6f7 d323f56 085a6f7 d323f56 085a6f7 d323f56 085a6f7 d323f56 b99f47a d323f56 befc6dd d323f56 085a6f7 d323f56 085a6f7 d323f56 085a6f7 d323f56 befc6dd d323f56 befc6dd |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077 1078 1079 1080 1081 1082 1083 1084 1085 1086 1087 1088 1089 1090 1091 1092 1093 1094 1095 1096 1097 1098 1099 1100 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 1116 1117 1118 1119 1120 1121 1122 1123 1124 1125 1126 1127 1128 1129 1130 1131 1132 1133 1134 1135 1136 1137 1138 1139 1140 1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 1161 1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 |
# smartheal_ai_processor.py
# Verbose, instrumented version β preserves public class/function names
# Turn on deep logging: export LOGLEVEL=DEBUG SMARTHEAL_DEBUG=1
import os
import logging
from datetime import datetime
from typing import Optional, Dict, List, Tuple
# ---- Environment defaults (do NOT globally hint CUDA here) ----
os.environ.setdefault("TOKENIZERS_PARALLELISM", "false")
LOGLEVEL = os.getenv("LOGLEVEL", "INFO").upper()
SMARTHEAL_DEBUG = os.getenv("SMARTHEAL_DEBUG", "0") == "1"
import cv2
import numpy as np
from PIL import Image
from PIL.ExifTags import TAGS
import spaces
# --- Logging config ---
logging.basicConfig(
level=getattr(logging, LOGLEVEL, logging.INFO),
format="%(asctime)s - %(levelname)s - %(message)s",
)
def _log_kv(prefix: str, kv: Dict):
logging.debug(prefix + " | " + " | ".join(f"{k}={v}" for k, v in kv.items()))
# ---- Paths / constants ----
UPLOADS_DIR = "uploads"
os.makedirs(UPLOADS_DIR, exist_ok=True)
HF_TOKEN = os.getenv("HF_TOKEN", None)
YOLO_MODEL_PATH = "src/best.pt"
SEG_MODEL_PATH = "src/segmentation_model_fixed.h5" # optional
GUIDELINE_PDFS = ["src/eHealth in Wound Care.pdf", "src/IWGDF Guideline.pdf", "src/evaluation.pdf"]
DATASET_ID = "SmartHeal/wound-image-uploads"
DEFAULT_PX_PER_CM = 38.0
PX_PER_CM_MIN, PX_PER_CM_MAX = 5.0, 1200.0
# Segmentation preprocessing knobs
SEG_EXPECTS_RGB = os.getenv("SEG_EXPECTS_RGB", "1") == "1" # most TF models trained on RGB
SEG_NORM = os.getenv("SEG_NORM", "0to1") # "0to1" | "imagenet"
SEG_THRESH = float(os.getenv("SEG_THRESH", "0.5"))
models_cache: Dict[str, object] = {}
knowledge_base_cache: Dict[str, object] = {}
# ---------- Utilities to prevent CUDA in main process ----------
from contextlib import contextmanager
@contextmanager
def _no_cuda_env():
"""
Mask GPUs so any library imported/constructed in the main process
cannot see CUDA (required for Spaces Stateless GPU).
"""
prev = os.environ.get("CUDA_VISIBLE_DEVICES")
os.environ["CUDA_VISIBLE_DEVICES"] = "-1"
try:
yield
finally:
if prev is None:
os.environ.pop("CUDA_VISIBLE_DEVICES", None)
else:
os.environ["CUDA_VISIBLE_DEVICES"] = prev
# ---------- Lazy imports (wrapped where needed) ----------
def _import_ultralytics():
# Prevent Ultralytics from probing CUDA on import
with _no_cuda_env():
from ultralytics import YOLO
return YOLO
def _import_tf_loader():
import tensorflow as tf
tf.config.set_visible_devices([], "GPU")
from tensorflow.keras.models import load_model
return load_model
def _import_hf_cls():
from transformers import pipeline
return pipeline
def _import_embeddings():
from langchain_community.embeddings import HuggingFaceEmbeddings
return HuggingFaceEmbeddings
def _import_langchain_pdf():
from langchain_community.document_loaders import PyPDFLoader
return PyPDFLoader
def _import_langchain_faiss():
from langchain_community.vectorstores import FAISS
return FAISS
def _import_hf_hub():
from huggingface_hub import HfApi, HfFolder
return HfApi, HfFolder
# ---------- SmartHeal prompts (system + user prefix) ----------
SMARTHEAL_SYSTEM_PROMPT = """\
You are SmartHeal Clinical Assistant, a wound-care decision-support system.
You analyze wound photographs and brief patient context to produce careful,
specific, guideline-informed recommendations WITHOUT diagnosing. You always:
- Use the measurements calculated by the vision pipeline as ground truth.
- Prefer concise, actionable steps tailored to exudate level, infection risk, and pain.
- Flag uncertainties and red flags that need escalation to a clinician.
- Avoid contraindicated advice; do not infer unseen comorbidities.
- Keep under 300 words and use the requested headings exactly.
- Tone: professional, clear, and conservative; no definitive medical claims.
- Safety: remind the user to seek clinician review for changes or red flags.
"""
SMARTHEAL_USER_PREFIX = """\
Patient: {patient_info}
Visual findings: type={wound_type}, size={length_cm}x{breadth_cm} cm, area={area_cm2} cm^2,
detection_conf={det_conf:.2f}, calibration={px_per_cm} px/cm.
Guideline context (snippets you can draw principles from; do not quote at length):
{guideline_context}
Write a structured answer with these headings exactly:
1. Clinical Summary (max 4 bullet points)
2. Likely Stage/Type (if uncertain, say 'uncertain')
3. Treatment Plan (specific dressing choices and frequency based on exudate/infection risk)
4. Red Flags (what to escalate and when)
5. Follow-up Cadence (days)
6. Notes (assumptions/uncertainties)
Keep to 220β300 words. Do NOT provide diagnosis. Avoid contraindicated advice.
"""
def _vlm_infer_gpu(messages, model_id: str, max_new_tokens: int, token: Optional[str]):
"""
Runs entirely inside a Spaces GPU worker. It's the ONLY place we allow CUDA init.
Safe for:
- CUDA device selection (no 'Invalid device id')
- BF16/FP16 choice via compute capability
- LLaVA processors with patch_size=None
- Processors WITHOUT a chat template (fallback to plain/LLaVA-style prompt)
"""
import logging
import torch
from typing import Optional, List
from transformers import (
AutoProcessor,
AutoModelForVision2Seq,
StoppingCriteria,
StoppingCriteriaList,
)
# -------- Device & dtype (robust) --------
def _pick_device_and_dtype():
if not torch.cuda.is_available() or torch.cuda.device_count() == 0:
logging.warning("CUDA not available; using CPU.")
return "cpu", torch.float32
idx = 0
try:
torch.cuda.set_device(idx)
except Exception as e:
logging.warning(f"torch.cuda.set_device({idx}) failed: {e}; falling back to CPU.")
return "cpu", torch.float32
device = f"cuda:{idx}"
try:
props = torch.cuda.get_device_properties(idx)
cc = props.major * 10 + props.minor
dtype = torch.bfloat16 if cc >= 80 else torch.float16
except Exception as e:
logging.warning(f"Could not query CUDA props: {e}; defaulting to float16.")
dtype = torch.float16
return device, dtype
device, torch_dtype = _pick_device_and_dtype()
# -------- Load model & processor --------
model = AutoModelForVision2Seq.from_pretrained(
model_id,
torch_dtype=torch_dtype,
trust_remote_code=True,
low_cpu_mem_usage=True,
token=token,
).to(device)
model.eval()
processor = AutoProcessor.from_pretrained(
model_id, trust_remote_code=True, token=token
)
# -------- Extract image & text --------
image_obj = None
text_prompt = ""
for m in messages:
if m.get("role") == "user":
for c in m.get("content", []):
if c.get("type") == "image":
image_obj = c.get("image")
elif c.get("type") == "text":
text_prompt = c.get("text", "")
break
if image_obj is None:
raise ValueError("No image found in messages for VLM inference.")
# -------- Normalize image to PIL --------
from PIL import Image
import numpy as np
def _to_pil(x):
if isinstance(x, Image.Image):
return x.convert("RGB")
if isinstance(x, str):
return Image.open(x).convert("RGB")
if isinstance(x, np.ndarray):
if x.ndim == 2:
x = np.stack([x]*3, axis=-1)
if x.dtype != np.uint8:
x = x.astype(np.uint8)
return Image.fromarray(x, "RGB")
if hasattr(x, "read"):
return Image.open(x).convert("RGB")
raise TypeError(f"Unsupported image type: {type(x)}")
image_pil = _to_pil(image_obj)
# -------- Ensure patch_size for LLaVA processors --------
def _ensure_patch_size(proc, mdl):
ps = getattr(proc, "patch_size", None)
if not ps:
candidates = [
getattr(getattr(mdl, "vision_tower", None), "config", None),
getattr(mdl.config, "vision_config", None),
getattr(proc, "image_processor", None),
getattr(getattr(proc, "image_processor", None), "config", None),
]
for obj in candidates:
if obj is None:
continue
maybe = getattr(obj, "patch_size", None)
if maybe:
ps = int(maybe); break
if not ps:
ps = 14 # safe default for ViT-L/14-style
try:
setattr(proc, "patch_size", ps)
except Exception:
pass
return ps
_ensure_patch_size(processor, model)
# -------- Build text (chat-template only if it truly exists) --------
# Some processors expose apply_chat_template but tokenizer has no template β ValueError. Guard it.
tokenizer = getattr(processor, "tokenizer", None)
has_template = bool(getattr(tokenizer, "chat_template", None))
used_chat_template = False
def _looks_like_llava():
name = processor.__class__.__name__.lower()
mid = (model_id or "").lower()
return ("llava" in name) or ("llava" in mid)
if hasattr(processor, "apply_chat_template") and has_template:
try:
chat = [{
"role": "user",
"content": [
{"type": "image", "image": image_pil},
{"type": "text", "text": text_prompt or "Describe the image."},
],
}]
text_for_model = processor.apply_chat_template(
chat, add_generation_prompt=True, tokenize=False
)
used_chat_template = True
except Exception as e:
logging.info(f"No usable chat template ({e}); falling back to plain prompt.")
text_for_model = (
f"USER: <image>\n{text_prompt or 'Describe the image.'}\nASSISTANT:"
if _looks_like_llava() else (text_prompt or "Describe the image.")
)
else:
text_for_model = (
f"USER: <image>\n{text_prompt or 'Describe the image.'}\nASSISTANT:"
if _looks_like_llava() else (text_prompt or "Describe the image.")
)
# -------- Tokenize --------
inputs = processor(
text=[text_for_model],
images=[image_pil],
return_tensors="pt",
padding=True,
).to(device)
# -------- Stopping criteria --------
class EosTokenCriteria(StoppingCriteria):
def __init__(self, eos_token_ids: List[int]):
import torch as _t
self.eos = _t.tensor(eos_token_ids, dtype=_t.long)
def __call__(self, input_ids, scores, **kwargs) -> bool:
import torch as _t
last_tok = input_ids[:, -1]
return _t.isin(last_tok, self.eos.to(last_tok.device)).any().item()
eos_ids: List[int] = []
if tokenizer is not None:
for attr in ("eos_token_id", "eot_token_id"):
v = getattr(tokenizer, attr, None)
if v is None: continue
eos_ids.extend([v] if isinstance(v, int) else list(v))
if not eos_ids:
cfg = getattr(model, "generation_config", None)
if cfg and getattr(cfg, "eos_token_id", None) is not None:
eos_ids = [cfg.eos_token_id]
else:
eos_ids = [2]
stopping_criteria = StoppingCriteriaList([EosTokenCriteria(eos_ids)])
if tokenizer is not None and getattr(tokenizer, "pad_token_id", None) is None:
try: tokenizer.pad_token_id = eos_ids[0]
except Exception: pass
# -------- Generate --------
gen_kwargs = dict(
max_new_tokens=int(max_new_tokens or 256),
do_sample=False,
stopping_criteria=stopping_criteria,
eos_token_id=eos_ids[0] if eos_ids else None,
pad_token_id=getattr(tokenizer, "pad_token_id", None) if tokenizer else None,
)
with torch.inference_mode():
out = model.generate(**inputs, **gen_kwargs)
# -------- Decode --------
seq = out[0]
if "input_ids" in inputs:
cut = inputs["input_ids"].shape[-1]
seq = seq[cut:]
if tokenizer is not None:
text_out = tokenizer.decode(seq, skip_special_tokens=True)
elif hasattr(processor, "batch_decode"):
text_out = processor.batch_decode(seq.unsqueeze(0), skip_special_tokens=True)[0]
else:
text_out = str(seq.tolist())
return text_out.strip()
def generate_medgemma_report(
patient_info: str,
visual_results: Dict,
guideline_context: str,
image_pil: Image.Image,
max_new_tokens: Optional[int] = None,
) -> str:
"""
MedGemma replacement using a vision-language model.
Loads & runs ONLY inside a GPU worker to satisfy Stateless GPU constraints.
"""
if os.getenv("SMARTHEAL_ENABLE_VLM", "1") != "1":
return "β οΈ VLM disabled"
model_id = os.getenv("SMARTHEAL_VLM_MODEL", "bczhou/tiny-llava-v1-hf")
max_new_tokens = max_new_tokens or int(os.getenv("SMARTHEAL_VLM_MAX_TOKENS", "600"))
uprompt = SMARTHEAL_USER_PREFIX.format(
patient_info=patient_info,
wound_type=visual_results.get("wound_type", "Unknown"),
length_cm=visual_results.get("length_cm", 0),
breadth_cm=visual_results.get("breadth_cm", 0),
area_cm2=visual_results.get("surface_area_cm2", 0),
det_conf=float(visual_results.get("detection_confidence", 0.0)),
px_per_cm=visual_results.get("px_per_cm", "?"),
guideline_context=(guideline_context or "")[:900],
)
# The `messages` structure is passed to the verified `_vlm_infer_gpu` function
messages = [
{"role": "system", "content": [{"type": "text", "text": SMARTHEAL_SYSTEM_PROMPT}]},
{"role": "user", "content": [
{"type": "image", "image": image_pil},
{"type": "text", "text": uprompt},
]},
]
try:
return _vlm_infer_gpu(messages, model_id, max_new_tokens, HF_TOKEN)
except Exception as e:
logging.error(f"VLM call failed: {e}", exc_info=True)
return f"β οΈ VLM error: {e}"
# ---------- Initialize CPU models ----------
def load_yolo_model():
YOLO = _import_ultralytics()
# Construct model with CUDA masked to avoid auto-selecting cuda:0
with _no_cuda_env():
model = YOLO(YOLO_MODEL_PATH)
return model
def load_segmentation_model():
import tensorflow as tf
load_model = _import_tf_loader()
return load_model(SEG_MODEL_PATH, compile=False, custom_objects={'InputLayer': tf.keras.layers.InputLayer})
def load_classification_pipeline():
pipe = _import_hf_cls()
return pipe("image-classification", model="Hemg/Wound-classification", token=HF_TOKEN, device="cpu")
def load_embedding_model():
Emb = _import_embeddings()
return Emb(model_name="sentence-transformers/all-MiniLM-L6-v2", model_kwargs={"device": "cpu"})
def initialize_cpu_models() -> None:
if HF_TOKEN:
try:
HfApi, HfFolder = _import_hf_hub()
HfFolder.save_token(HF_TOKEN)
logging.info("β
HF token set")
except Exception as e:
logging.warning(f"HF token save failed: {e}")
if "det" not in models_cache:
try:
models_cache["det"] = load_yolo_model()
logging.info("β
YOLO loaded (CPU; CUDA masked in main)")
except Exception as e:
logging.error(f"YOLO load failed: {e}")
if "seg" not in models_cache:
try:
if os.path.exists(SEG_MODEL_PATH):
models_cache["seg"] = load_segmentation_model()
m = models_cache["seg"]
ishape = getattr(m, "input_shape", None)
oshape = getattr(m, "output_shape", None)
logging.info(f"β
Segmentation model loaded (CPU) | input_shape={ishape} output_shape={oshape}")
else:
models_cache["seg"] = None
logging.warning("Segmentation model file missing; skipping.")
except Exception as e:
models_cache["seg"] = None
logging.warning(f"Segmentation unavailable: {e}")
if "cls" not in models_cache:
try:
models_cache["cls"] = load_classification_pipeline()
logging.info("β
Classifier loaded (CPU)")
except Exception as e:
models_cache["cls"] = None
logging.warning(f"Classifier unavailable: {e}")
if "embedding_model" not in models_cache:
try:
models_cache["embedding_model"] = load_embedding_model()
logging.info("β
Embeddings loaded (CPU)")
except Exception as e:
models_cache["embedding_model"] = None
logging.warning(f"Embeddings unavailable: {e}")
def setup_knowledge_base() -> None:
if "vector_store" in knowledge_base_cache:
return
docs: List = []
try:
PyPDFLoader = _import_langchain_pdf()
for pdf in GUIDELINE_PDFS:
if os.path.exists(pdf):
try:
docs.extend(PyPDFLoader(pdf).load())
logging.info(f"Loaded PDF: {pdf}")
except Exception as e:
logging.warning(f"PDF load failed ({pdf}): {e}")
except Exception as e:
logging.warning(f"LangChain PDF loader unavailable: {e}")
if docs and models_cache.get("embedding_model"):
try:
from langchain.text_splitter import RecursiveCharacterTextSplitter
FAISS = _import_langchain_faiss()
chunks = RecursiveCharacterTextSplitter(chunk_size=1000, chunk_overlap=100).split_documents(docs)
knowledge_base_cache["vector_store"] = FAISS.from_documents(chunks, models_cache["embedding_model"])
logging.info(f"β
Knowledge base ready ({len(chunks)} chunks)")
except Exception as e:
knowledge_base_cache["vector_store"] = None
logging.warning(f"KB build failed: {e}")
else:
knowledge_base_cache["vector_store"] = None
logging.warning("KB disabled (no docs or embeddings).")
initialize_cpu_models()
setup_knowledge_base()
# ---------- Calibration helpers ----------
def _exif_to_dict(pil_img: Image.Image) -> Dict[str, object]:
out = {}
try:
exif = pil_img.getexif()
if not exif:
return out
for k, v in exif.items():
tag = TAGS.get(k, k)
out[tag] = v
except Exception:
pass
return out
def _to_float(val) -> Optional[float]:
try:
if val is None:
return None
if isinstance(val, tuple) and len(val) == 2:
num, den = float(val[0]), float(val[1]) if float(val[1]) != 0 else 1.0
return num / den
return float(val)
except Exception:
return None
def _estimate_sensor_width_mm(f_mm: Optional[float], f35: Optional[float]) -> Optional[float]:
if f_mm and f35 and f35 > 0:
return 36.0 * f_mm / f35
return None
def estimate_px_per_cm_from_exif(pil_img: Image.Image, default_px_per_cm: float = DEFAULT_PX_PER_CM) -> Tuple[float, Dict]:
meta = {"used": "default", "f_mm": None, "f35": None, "sensor_w_mm": None, "distance_m": None}
try:
exif = _exif_to_dict(pil_img)
f_mm = _to_float(exif.get("FocalLength"))
f35 = _to_float(exif.get("FocalLengthIn35mmFilm") or exif.get("FocalLengthIn35mm"))
subj_dist_m = _to_float(exif.get("SubjectDistance"))
sensor_w_mm = _estimate_sensor_width_mm(f_mm, f35)
meta.update({"f_mm": f_mm, "f35": f35, "sensor_w_mm": sensor_w_mm, "distance_m": subj_dist_m})
if f_mm and sensor_w_mm and subj_dist_m and subj_dist_m > 0:
w_px = pil_img.width
field_w_mm = sensor_w_mm * (subj_dist_m * 1000.0) / f_mm
field_w_cm = field_w_mm / 10.0
px_per_cm = w_px / max(field_w_cm, 1e-6)
px_per_cm = float(np.clip(px_per_cm, PX_PER_CM_MIN, PX_PER_CM_MAX))
meta["used"] = "exif"
return px_per_cm, meta
return float(default_px_per_cm), meta
except Exception:
return float(default_px_per_cm), meta
# ---------- Segmentation helpers ----------
def _imagenet_norm(arr: np.ndarray) -> np.ndarray:
mean = np.array([123.675, 116.28, 103.53], dtype=np.float32)
std = np.array([58.395, 57.12, 57.375], dtype=np.float32)
return (arr.astype(np.float32) - mean) / std
def _preprocess_for_seg(bgr_roi: np.ndarray, target_hw: Tuple[int, int]) -> np.ndarray:
H, W = target_hw
resized = cv2.resize(bgr_roi, (W, H), interpolation=cv2.INTER_LINEAR)
if SEG_EXPECTS_RGB:
resized = cv2.cvtColor(resized, cv2.COLOR_BGR2RGB)
if SEG_NORM.lower() == "imagenet":
x = _imagenet_norm(resized)
else:
x = resized.astype(np.float32) / 255.0
x = np.expand_dims(x, axis=0) # (1,H,W,3)
return x
def _to_prob(pred: np.ndarray) -> np.ndarray:
p = np.squeeze(pred)
pmin, pmax = float(p.min()), float(p.max())
if pmax > 1.0 or pmin < 0.0:
p = 1.0 / (1.0 + np.exp(-p))
return p.astype(np.float32)
# ---- Adaptive threshold + GrabCut grow ----
def _adaptive_prob_threshold(p: np.ndarray) -> float:
"""
Choose a threshold that avoids tiny blobs while not swallowing skin.
Try Otsu and the 90th percentile, clamp to [0.25, 0.65], pick by area heuristic.
"""
p01 = np.clip(p.astype(np.float32), 0, 1)
p255 = (p01 * 255).astype(np.uint8)
ret_otsu, _ = cv2.threshold(p255, 0, 255, cv2.THRESH_BINARY + cv2.THRESH_OTSU)
thr_otsu = float(np.clip(ret_otsu / 255.0, 0.25, 0.65))
thr_pctl = float(np.clip(np.percentile(p01, 90), 0.25, 0.65))
def area_frac(thr: float) -> float:
return float((p01 >= thr).sum()) / float(p01.size)
af_otsu = area_frac(thr_otsu)
af_pctl = area_frac(thr_pctl)
def score(af: float) -> float:
target_low, target_high = 0.03, 0.10
if af < target_low: return abs(af - target_low) * 3.0
if af > target_high: return abs(af - target_high) * 1.5
return 0.0
return thr_otsu if score(af_otsu) <= score(af_pctl) else thr_pctl
def _grabcut_refine(bgr: np.ndarray, seed01: np.ndarray, iters: int = 3) -> np.ndarray:
"""Grow from a confident core into low-contrast margins."""
h, w = bgr.shape[:2]
gc = np.full((h, w), cv2.GC_PR_BGD, np.uint8)
k = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (5, 5))
seed_dil = cv2.dilate(seed01, k, iterations=1)
gc[seed01.astype(bool)] = cv2.GC_PR_FGD
gc[seed_dil.astype(bool)] = cv2.GC_FGD
gc[0, :], gc[-1, :], gc[:, 0], gc[:, 1] = cv2.GC_BGD, cv2.GC_BGD, cv2.GC_BGD, cv2.GC_BGD
bgdModel = np.zeros((1, 65), np.float64)
fgdModel = np.zeros((1, 65), np.float64)
cv2.grabCut(bgr, gc, None, bgdModel, fgdModel, iters, cv2.GC_INIT_WITH_MASK)
return np.where((gc == cv2.GC_FGD) | (gc == cv2.GC_PR_FGD), 1, 0).astype(np.uint8)
def _fill_holes(mask01: np.ndarray) -> np.ndarray:
h, w = mask01.shape[:2]
ff = np.zeros((h + 2, w + 2), np.uint8)
m = (mask01 * 255).astype(np.uint8).copy()
cv2.floodFill(m, ff, (0, 0), 255)
m_inv = cv2.bitwise_not(m)
out = ((mask01 * 255) | m_inv) // 255
return out.astype(np.uint8)
def _clean_mask(mask01: np.ndarray) -> np.ndarray:
"""Open β Close β Fill holes β Largest component (no dilation)."""
mask01 = (mask01 > 0).astype(np.uint8)
k3 = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (3, 3))
k5 = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (5, 5))
mask01 = cv2.morphologyEx(mask01, cv2.MORPH_OPEN, k3, iterations=1)
mask01 = cv2.morphologyEx(mask01, cv2.MORPH_CLOSE, k5, iterations=1)
mask01 = _fill_holes(mask01)
# Keep largest component only
num, labels, stats, _ = cv2.connectedComponentsWithStats(mask01, 8)
if num > 1:
areas = stats[1:, cv2.CC_STAT_AREA]
if areas.size:
largest_idx = 1 + int(np.argmax(areas))
mask01 = (labels == largest_idx).astype(np.uint8)
return (mask01 > 0).astype(np.uint8)
# Global last debug dict (per-process)
_last_seg_debug: Dict[str, object] = {}
def segment_wound(image_bgr: np.ndarray, ts: str, out_dir: str) -> Tuple[np.ndarray, Dict[str, object]]:
"""
TF model β adaptive threshold on prob β GrabCut grow β cleanup.
Fallback: KMeans-Lab.
Returns (mask_uint8_0_255, debug_dict)
"""
debug = {"used": None, "reason": None, "positive_fraction": 0.0,
"thr": None, "heatmap_path": None, "roi_seen_by_model": None}
seg_model = models_cache.get("seg", None)
# --- Model path ---
if seg_model is not None:
try:
ishape = getattr(seg_model, "input_shape", None)
if not ishape or len(ishape) < 4:
raise ValueError(f"Bad seg input_shape: {ishape}")
th, tw = int(ishape[1]), int(ishape[2])
x = _preprocess_for_seg(image_bgr, (th, tw))
roi_seen_path = None
if SMARTHEAL_DEBUG:
roi_seen_path = os.path.join(out_dir, f"roi_for_seg_{ts}.png")
cv2.imwrite(roi_seen_path, image_bgr)
pred = seg_model.predict(x, verbose=0)
if isinstance(pred, (list, tuple)): pred = pred[0]
p = _to_prob(pred)
p = cv2.resize(p, (image_bgr.shape[1], image_bgr.shape[0]), interpolation=cv2.INTER_LINEAR)
heatmap_path = None
if SMARTHEAL_DEBUG:
hm = (np.clip(p, 0, 1) * 255).astype(np.uint8)
heat = cv2.applyColorMap(hm, cv2.COLORMAP_JET)
heatmap_path = os.path.join(out_dir, f"seg_pred_heatmap_{ts}.png")
cv2.imwrite(heatmap_path, heat)
thr = _adaptive_prob_threshold(p)
core01 = (p >= thr).astype(np.uint8)
core_frac = float(core01.sum()) / float(core01.size)
if core_frac < 0.005:
thr2 = max(thr - 0.10, 0.15)
core01 = (p >= thr2).astype(np.uint8)
thr = thr2
core_frac = float(core01.sum()) / float(core01.size)
if core01.any():
gc01 = _grabcut_refine(image_bgr, core01, iters=3)
mask01 = _clean_mask(gc01)
else:
mask01 = np.zeros(core01.shape, np.uint8)
pos_frac = float(mask01.sum()) / float(mask01.size)
logging.info(f"SegModel USED | thr={float(thr):.2f} core_frac={core_frac:.4f} final_frac={pos_frac:.4f}")
debug.update({
"used": "tf_model",
"reason": "ok",
"positive_fraction": pos_frac,
"thr": float(thr),
"heatmap_path": heatmap_path,
"roi_seen_by_model": roi_seen_path
})
return (mask01 * 255).astype(np.uint8), debug
except Exception as e:
logging.warning(f"β οΈ Segmentation model failed β fallback. Reason: {e}")
debug.update({"used": "fallback_kmeans", "reason": f"model_failed: {e}"})
# --- Fallback: KMeans in Lab (reddest cluster as wound) ---
Z = image_bgr.reshape((-1, 3)).astype(np.float32)
criteria = (cv2.TERM_CRITERIA_EPS + cv2.TERM_CRITERIA_MAX_ITER, 10, 1.0)
_, labels, centers = cv2.kmeans(Z, 2, None, criteria, 5, cv2.KMEANS_PP_CENTERS)
centers_u8 = centers.astype(np.uint8).reshape(1, 2, 3)
centers_lab = cv2.cvtColor(centers_u8, cv2.COLOR_BGR2LAB)[0]
wound_idx = int(np.argmax(centers_lab[:, 1])) # maximize a* (red)
mask01 = (labels.reshape(image_bgr.shape[:2]) == wound_idx).astype(np.uint8)
mask01 = _clean_mask(mask01)
pos_frac = float(mask01.sum()) / float(mask01.size)
logging.info(f"KMeans USED | final_frac={pos_frac:.4f}")
debug.update({
"used": "fallback_kmeans",
"reason": debug.get("reason") or "no_model",
"positive_fraction": pos_frac,
"thr": None
})
return (mask01 * 255).astype(np.uint8), debug
# ---------- Measurement + overlay helpers ----------
def largest_component_mask(binary01: np.ndarray, min_area_px: int = 50) -> np.ndarray:
num, labels, stats, _ = cv2.connectedComponentsWithStats(binary01.astype(np.uint8), connectivity=8)
if num <= 1:
return binary01.astype(np.uint8)
areas = stats[1:, cv2.CC_STAT_AREA]
if areas.size == 0 or areas.max() < min_area_px:
return binary01.astype(np.uint8)
largest_idx = 1 + int(np.argmax(areas))
return (labels == largest_idx).astype(np.uint8)
def measure_min_area_rect(mask01: np.ndarray, px_per_cm: float) -> Tuple[float, float, Tuple]:
contours, _ = cv2.findContours(mask01.astype(np.uint8), cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
if not contours:
return 0.0, 0.0, (None, None)
cnt = max(contours, key=cv2.contourArea)
rect = cv2.minAreaRect(cnt)
(w_px, h_px) = rect[1]
length_px, breadth_px = (max(w_px, h_px), min(w_px, h_px))
length_cm = round(length_px / max(px_per_cm, 1e-6), 2)
breadth_cm = round(breadth_px / max(px_per_cm, 1e-6), 2)
box = cv2.boxPoints(rect).astype(int)
return length_cm, breadth_cm, (box, rect[0])
def area_cm2_from_contour(mask01: np.ndarray, px_per_cm: float) -> Tuple[float, Optional[np.ndarray]]:
"""Area from largest polygon (sub-pixel); returns (area_cm2, contour)."""
m = (mask01 > 0).astype(np.uint8)
contours, _ = cv2.findContours(m, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
if not contours:
return 0.0, None
cnt = max(contours, key=cv2.contourArea)
poly_area_px2 = float(cv2.contourArea(cnt))
area_cm2 = round(poly_area_px2 / (max(px_per_cm, 1e-6) ** 2), 2)
return area_cm2, cnt
def clamp_area_with_minrect(cnt: np.ndarray, px_per_cm: float, area_cm2_poly: float) -> float:
rect = cv2.minAreaRect(cnt)
(w_px, h_px) = rect[1]
rect_area_px2 = float(max(w_px, 0.0) * max(h_px, 0.0))
rect_area_cm2 = rect_area_px2 / (max(px_per_cm, 1e-6) ** 2)
return round(min(area_cm2_poly, rect_area_cm2 * 1.05), 2)
def draw_measurement_overlay(
base_bgr: np.ndarray,
mask01: np.ndarray,
rect_box: np.ndarray,
length_cm: float,
breadth_cm: float,
thickness: int = 2
) -> np.ndarray:
"""
1) Strong red mask overlay + white contour
2) Min-area rectangle
3) Double-headed arrows labeled Length/Width
"""
overlay = base_bgr.copy()
# Mask tint
mask255 = (mask01 * 255).astype(np.uint8)
mask3 = cv2.merge([mask255, mask255, mask255])
red = np.zeros_like(overlay); red[:] = (0, 0, 255)
alpha = 0.55
tinted = cv2.addWeighted(overlay, 1 - alpha, red, alpha, 0)
overlay = np.where(mask3 > 0, tinted, overlay)
# Contour
cnts, _ = cv2.findContours(mask255, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
if cnts:
cv2.drawContours(overlay, cnts, -1, (255, 255, 255), 2)
if rect_box is not None:
cv2.polylines(overlay, [rect_box], True, (255, 255, 255), thickness)
pts = rect_box.reshape(-1, 2)
def midpoint(a, b): return (int((a[0] + b[0]) / 2), int((a[1] + b[1]) / 2))
e = [np.linalg.norm(pts[i] - pts[(i + 1) % 4]) for i in range(4)]
long_edge_idx = int(np.argmax(e))
mids = [midpoint(pts[i], pts[(i + 1) % 4]) for i in range(4)]
long_pair = (long_edge_idx, (long_edge_idx + 2) % 4)
short_pair = ((long_edge_idx + 1) % 4, (long_edge_idx + 3) % 4)
def draw_double_arrow(img, p1, p2):
cv2.arrowedLine(img, p1, p2, (0, 0, 0), thickness + 2, tipLength=0.05)
cv2.arrowedLine(img, p2, p1, (0, 0, 0), thickness + 2, tipLength=0.05)
cv2.arrowedLine(img, p1, p2, (255, 255, 255), thickness, tipLength=0.05)
cv2.arrowedLine(img, p2, p1, (255, 255, 255), thickness, tipLength=0.05)
def put_label(text, anchor):
org = (anchor[0] + 6, anchor[1] - 6)
cv2.putText(overlay, text, org, cv2.FONT_HERSHEY_SIMPLEX, 0.7, (0, 0, 0), 4, cv2.LINE_AA)
cv2.putText(overlay, text, org, cv2.FONT_HERSHEY_SIMPLEX, 0.7, (255, 255, 255), 2, cv2.LINE_AA)
draw_double_arrow(overlay, mids[long_pair[0]], mids[long_pair[1]])
draw_double_arrow(overlay, mids[short_pair[0]], mids[short_pair[1]])
put_label(f"Length: {length_cm:.2f} cm", mids[long_pair[0]])
put_label(f"Width: {breadth_cm:.2f} cm", mids[short_pair[0]])
return overlay
# ---------- AI PROCESSOR ----------
class AIProcessor:
def __init__(self):
self.models_cache = models_cache
self.knowledge_base_cache = knowledge_base_cache
self.uploads_dir = UPLOADS_DIR
self.dataset_id = DATASET_ID
self.hf_token = HF_TOKEN
def _ensure_analysis_dir(self) -> str:
out_dir = os.path.join(self.uploads_dir, "analysis")
os.makedirs(out_dir, exist_ok=True)
return out_dir
def perform_visual_analysis(self, image_pil: Image.Image) -> Dict:
"""
YOLO detect β crop ROI β segment_wound(ROI) β clean mask β
minAreaRect measurement (cm) using EXIF px/cm β save outputs.
"""
try:
px_per_cm, exif_meta = estimate_px_per_cm_from_exif(image_pil, DEFAULT_PX_PER_CM)
# Guardrails for calibration to avoid huge area blow-ups
px_per_cm = float(np.clip(px_per_cm, 20.0, 350.0))
if (exif_meta or {}).get("used") != "exif":
logging.warning(f"Calibration fallback used: px_per_cm={px_per_cm:.2f} (default). Prefer ruler/Aruco for accuracy.")
image_cv = cv2.cvtColor(np.array(image_pil.convert("RGB")), cv2.COLOR_RGB2BGR)
# --- Detection ---
det_model = self.models_cache.get("det")
if det_model is None:
raise RuntimeError("YOLO model not loaded")
# Force CPU inference and avoid CUDA touch
results = det_model.predict(image_cv, verbose=False, device="cpu")
if (not results) or (not getattr(results[0], "boxes", None)) or (len(results[0].boxes) == 0):
try:
import gradio as gr
raise gr.Error("No wound could be detected.")
except Exception:
raise RuntimeError("No wound could be detected.")
box = results[0].boxes[0].xyxy[0].cpu().numpy().astype(int)
x1, y1, x2, y2 = [int(v) for v in box]
x1, y1 = max(0, x1), max(0, y1)
x2, y2 = min(image_cv.shape[1], x2), min(image_cv.shape[0], y2)
roi = image_cv[y1:y2, x1:x2].copy()
if roi.size == 0:
try:
import gradio as gr
raise gr.Error("Detected ROI is empty.")
except Exception:
raise RuntimeError("Detected ROI is empty.")
out_dir = self._ensure_analysis_dir()
ts = datetime.now().strftime("%Y%m%d_%H%M%S")
# --- Segmentation (model-first + KMeans fallback) ---
mask_u8_255, seg_debug = segment_wound(roi, ts, out_dir)
mask01 = (mask_u8_255 > 127).astype(np.uint8)
if mask01.any():
mask01 = _clean_mask(mask01)
logging.debug(f"Mask postproc: px_after={int(mask01.sum())}")
# --- Measurement (accurate & conservative) ---
if mask01.any():
length_cm, breadth_cm, (box_pts, _) = measure_min_area_rect(mask01, px_per_cm)
area_poly_cm2, largest_cnt = area_cm2_from_contour(mask01, px_per_cm)
if largest_cnt is not None:
surface_area_cm2 = clamp_area_with_minrect(largest_cnt, px_per_cm, area_poly_cm2)
else:
surface_area_cm2 = area_poly_cm2
anno_roi = draw_measurement_overlay(roi, mask01, box_pts, length_cm, breadth_cm)
segmentation_empty = False
else:
# Fallback if seg failed: use ROI dimensions
h_px = max(0, y2 - y1); w_px = max(0, x2 - x1)
length_cm = round(max(h_px, w_px) / px_per_cm, 2)
breadth_cm = round(min(h_px, w_px) / px_per_cm, 2)
surface_area_cm2 = round((h_px * w_px) / (px_per_cm ** 2), 2)
anno_roi = roi.copy()
cv2.rectangle(anno_roi, (2, 2), (anno_roi.shape[1]-3, anno_roi.shape[0]-3), (0, 0, 255), 3)
cv2.line(anno_roi, (0, 0), (anno_roi.shape[1]-1, anno_roi.shape[0]-1), (0, 0, 255), 2)
cv2.line(anno_roi, (anno_roi.shape[1]-1, 0), (0, anno_roi.shape[0]-1), (0, 0, 255), 2)
box_pts = None
segmentation_empty = True
# --- Save visualizations ---
original_path = os.path.join(out_dir, f"original_{ts}.png")
cv2.imwrite(original_path, image_cv)
det_vis = image_cv.copy()
cv2.rectangle(det_vis, (x1, y1), (x2, y2), (0, 255, 0), 2)
detection_path = os.path.join(out_dir, f"detection_{ts}.png")
cv2.imwrite(detection_path, det_vis)
roi_mask_path = os.path.join(out_dir, f"roi_mask_{ts}.png")
cv2.imwrite(roi_mask_path, (mask01 * 255).astype(np.uint8))
# ROI overlay (mask tint + contour, without arrows)
mask255 = (mask01 * 255).astype(np.uint8)
mask3 = cv2.merge([mask255, mask255, mask255])
red = np.zeros_like(roi); red[:] = (0, 0, 255)
alpha = 0.55
tinted = cv2.addWeighted(roi, 1 - alpha, red, alpha, 0)
if mask255.any():
roi_overlay = np.where(mask3 > 0, tinted, roi)
cnts, _ = cv2.findContours(mask255, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
cv2.drawContours(roi_overlay, cnts, -1, (255, 255, 255), 2)
else:
roi_overlay = anno_roi
seg_full = image_cv.copy()
seg_full[y1:y2, x1:x2] = roi_overlay
segmentation_path = os.path.join(out_dir, f"segmentation_{ts}.png")
cv2.imwrite(segmentation_path, seg_full)
segmentation_roi_path = os.path.join(out_dir, f"segmentation_roi_{ts}.png")
cv2.imwrite(segmentation_roi_path, roi_overlay)
# Annotated (mask + arrows + labels) in full-frame
anno_full = image_cv.copy()
anno_full[y1:y2, x1:x2] = anno_roi
annotated_seg_path = os.path.join(out_dir, f"segmentation_annotated_{ts}.png")
cv2.imwrite(annotated_seg_path, anno_full)
# --- Optional classification ---
wound_type = "Unknown"
cls_pipe = self.models_cache.get("cls")
if cls_pipe is not None:
try:
preds = cls_pipe(Image.fromarray(cv2.cvtColor(roi, cv2.COLOR_BGR2RGB)))
if preds:
wound_type = max(preds, key=lambda x: x.get("score", 0)).get("label", "Unknown")
except Exception as e:
logging.warning(f"Classification failed: {e}")
# Log end-of-seg summary
seg_summary = {
"seg_used": seg_debug.get("used"),
"seg_reason": seg_debug.get("reason"),
"positive_fraction": round(float(seg_debug.get("positive_fraction", 0.0)), 6),
"threshold": seg_debug.get("thr"),
"segmentation_empty": segmentation_empty,
"exif_px_per_cm": round(px_per_cm, 3),
}
_log_kv("SEG_SUMMARY", seg_summary)
return {
"wound_type": wound_type,
"length_cm": length_cm,
"breadth_cm": breadth_cm,
"surface_area_cm2": surface_area_cm2,
"px_per_cm": round(px_per_cm, 2),
"calibration_meta": exif_meta,
"detection_confidence": float(results[0].boxes.conf[0].cpu().item())
if getattr(results[0].boxes, "conf", None) is not None else 0.0,
"detection_image_path": detection_path,
"segmentation_image_path": annotated_seg_path,
"segmentation_annotated_path": annotated_seg_path,
"segmentation_roi_path": segmentation_roi_path,
"roi_mask_path": roi_mask_path,
"segmentation_empty": segmentation_empty,
"segmentation_debug": seg_debug,
"original_image_path": original_path,
}
except Exception as e:
logging.error(f"Visual analysis failed: {e}", exc_info=True)
raise
# ---------- Knowledge base + reporting ----------
def query_guidelines(self, query: str) -> str:
try:
vs = self.knowledge_base_cache.get("vector_store")
if not vs:
return "Knowledge base is not available."
retriever = vs.as_retriever(search_kwargs={"k": 5})
# Modern API (avoid get_relevant_documents deprecation)
docs = retriever.invoke(query)
lines: List[str] = []
for d in docs:
src = (d.metadata or {}).get("source", "N/A")
txt = (d.page_content or "")[:300]
lines.append(f"Source: {src}\nContent: {txt}...")
return "\n\n".join(lines) if lines else "No relevant guideline snippets found."
except Exception as e:
logging.warning(f"Guidelines query failed: {e}")
return f"Guidelines query failed: {str(e)}"
def _generate_fallback_report(self, patient_info: str, visual_results: Dict, guideline_context: str) -> str:
return f"""# π©Ί SmartHeal AI - Comprehensive Wound Analysis Report
## π Patient Information
{patient_info}
## π Visual Analysis Results
- **Wound Type**: {visual_results.get('wound_type', 'Unknown')}
- **Dimensions**: {visual_results.get('length_cm', 0)} cm Γ {visual_results.get('breadth_cm', 0)} cm
- **Surface Area**: {visual_results.get('surface_area_cm2', 0)} cmΒ²
- **Detection Confidence**: {visual_results.get('detection_confidence', 0):.1%}
- **Calibration**: {visual_results.get('px_per_cm','?')} px/cm ({(visual_results.get('calibration_meta') or {}).get('used','default')})
## π Analysis Images
- **Original**: {visual_results.get('original_image_path', 'N/A')}
- **Detection**: {visual_results.get('detection_image_path', 'N/A')}
- **Segmentation**: {visual_results.get('segmentation_image_path', 'N/A')}
- **Annotated**: {visual_results.get('segmentation_annotated_path', 'N/A')}
## π― Clinical Summary
Automated analysis provides quantitative measurements; verify via clinical examination.
## π Recommendations
- Cleanse wound gently; select dressing per exudate/infection risk
- Debride necrotic tissue if indicated (clinical decision)
- Document with serial photos and measurements
## π
Monitoring
- Daily in week 1, then every 2β3 days (or as indicated)
- Weekly progress review
## π Guideline Context
{(guideline_context or '')[:800]}{"..." if guideline_context and len(guideline_context) > 800 else ''}
**Disclaimer:** Automated, for decision support only. Verify clinically.
"""
def generate_final_report(
self,
patient_info: str,
visual_results: Dict,
guideline_context: str,
image_pil: Image.Image,
max_new_tokens: Optional[int] = None,
) -> str:
try:
report = generate_medgemma_report(
patient_info, visual_results, guideline_context, image_pil, max_new_tokens
)
if report and report.strip() and not report.startswith(("β οΈ", "β")):
return report
logging.warning("VLM unavailable/invalid; using fallback.")
return self._generate_fallback_report(patient_info, visual_results, guideline_context)
except Exception as e:
logging.error(f"Report generation failed: {e}")
return self._generate_fallback_report(patient_info, visual_results, guideline_context)
def save_and_commit_image(self, image_pil: Image.Image) -> str:
try:
os.makedirs(self.uploads_dir, exist_ok=True)
ts = datetime.now().strftime("%Y%m%d_%H%M%S")
filename = f"{ts}.png"
path = os.path.join(self.uploads_dir, filename)
image_pil.convert("RGB").save(path)
logging.info(f"β
Image saved locally: {path}")
if HF_TOKEN and DATASET_ID:
try:
HfApi, HfFolder = _import_hf_hub()
HfFolder.save_token(HF_TOKEN)
api = HfApi()
api.upload_file(
path_or_fileobj=path,
path_in_repo=f"images/{filename}",
repo_id=DATASET_ID,
repo_type="dataset",
token=HF_TOKEN,
commit_message=f"Upload wound image: {filename}",
)
logging.info("β
Image committed to HF dataset")
except Exception as e:
logging.warning(f"HF upload failed: {e}")
return path
except Exception as e:
logging.error(f"Failed to save/commit image: {e}")
return ""
def full_analysis_pipeline(self, image_pil: Image.Image, questionnaire_data: Dict) -> Dict:
try:
saved_path = self.save_and_commit_image(image_pil)
visual_results = self.perform_visual_analysis(image_pil)
pi = questionnaire_data or {}
patient_info = (
f"Age: {pi.get('age','N/A')}, "
f"Diabetic: {pi.get('diabetic','N/A')}, "
f"Allergies: {pi.get('allergies','N/A')}, "
f"Date of Wound: {pi.get('date_of_injury','N/A')}, "
f"Professional Care: {pi.get('professional_care','N/A')}, "
f"Oozing/Bleeding: {pi.get('oozing_bleeding','N/A')}, "
f"Infection: {pi.get('infection','N/A')}, "
f"Moisture: {pi.get('moisture','N/A')}"
)
query = (
f"best practices for managing a {visual_results.get('wound_type','Unknown')} "
f"with moisture '{pi.get('moisture','unknown')}' and infection '{pi.get('infection','unknown')}' "
f"in a diabetic status '{pi.get('diabetic','unknown')}'"
)
guideline_context = self.query_guidelines(query)
report = self.generate_final_report(patient_info, visual_results, guideline_context, image_pil)
return {
"success": True,
"visual_analysis": visual_results,
"report": report,
"saved_image_path": saved_path,
"guideline_context": (guideline_context or "")[:500] + (
"..." if guideline_context and len(guideline_context) > 500 else ""
),
}
except Exception as e:
logging.error(f"Pipeline error: {e}")
return {
"success": False,
"error": str(e),
"visual_analysis": {},
"report": f"Analysis failed: {str(e)}",
"saved_image_path": None,
"guideline_context": "",
}
def analyze_wound(self, image, questionnaire_data: Dict) -> Dict:
try:
if isinstance(image, str):
if not os.path.exists(image):
raise ValueError(f"Image file not found: {image}")
image_pil = Image.open(image)
elif isinstance(image, Image.Image):
image_pil = image
elif isinstance(image, np.ndarray):
image_pil = Image.fromarray(image)
else:
raise ValueError(f"Unsupported image type: {type(image)}")
return self.full_analysis_pipeline(image_pil, questionnaire_data or {})
except Exception as e:
logging.error(f"Wound analysis error: {e}")
return {
"success": False,
"error": str(e),
"visual_analysis": {},
"report": f"Analysis initialization failed: {str(e)}",
"saved_image_path": None,
"guideline_context": "",
} |