SmartHeal-Agentic-AI / src /ai_processor.py
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# smartheal_ai_processor.py
# Verbose, instrumented version — 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 220–300 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 → 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 "⚠️ 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"⚠️ 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("✅ 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("✅ 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"✅ 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("✅ 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("✅ 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"✅ 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 → Close → Fill holes → 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 → adaptive threshold on prob → GrabCut grow → 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"⚠️ Segmentation model failed → 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 → crop ROI → segment_wound(ROI) → clean mask →
minAreaRect measurement (cm) using EXIF px/cm → 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"""# 🩺 SmartHeal AI - Comprehensive Wound Analysis Report
## 📋 Patient Information
{patient_info}
## 🔍 Visual Analysis Results
- **Wound Type**: {visual_results.get('wound_type', 'Unknown')}
- **Dimensions**: {visual_results.get('length_cm', 0)} cm × {visual_results.get('breadth_cm', 0)} cm
- **Surface Area**: {visual_results.get('surface_area_cm2', 0)} cm²
- **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')})
## 📊 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')}
## 🎯 Clinical Summary
Automated analysis provides quantitative measurements; verify via clinical examination.
## 💊 Recommendations
- Cleanse wound gently; select dressing per exudate/infection risk
- Debride necrotic tissue if indicated (clinical decision)
- Document with serial photos and measurements
## 📅 Monitoring
- Daily in week 1, then every 2–3 days (or as indicated)
- Weekly progress review
## 📚 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(("⚠️", "❌")):
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"✅ 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("✅ 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": "",
}