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Update app.py
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app.py
CHANGED
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# Verbose, instrumented version — preserves public class/function names
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# Turn on deep logging: export LOGLEVEL=DEBUG SMARTHEAL_DEBUG=1
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import os
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import logging
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#
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from PIL import Image
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from PIL.ExifTags import TAGS
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logging.basicConfig(
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level=getattr(logging, LOGLEVEL, logging.INFO),
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format="%(asctime)s - %(levelname)s - %(message)s",
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)
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def _log_kv(prefix: str, kv: Dict):
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logging.debug(prefix + " | " + " | ".join(f"{k}={v}" for k, v in kv.items()))
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# --- Spaces GPU decorator (REQUIRED) ---
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from spaces import GPU as _SPACES_GPU
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@_SPACES_GPU(enable_queue=True)
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def smartheal_gpu_stub(ping: int = 0) -> str:
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return "ready"
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# ---- Paths / constants ----
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UPLOADS_DIR = "uploads"
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os.makedirs(UPLOADS_DIR, exist_ok=True)
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HF_TOKEN = os.getenv("HF_TOKEN", None)
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YOLO_MODEL_PATH = "src/best.pt"
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SEG_MODEL_PATH = "src/segmentation_model.h5" # optional; legacy .h5 supported
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GUIDELINE_PDFS = ["src/eHealth in Wound Care.pdf", "src/IWGDF Guideline.pdf", "src/evaluation.pdf"]
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DATASET_ID = "SmartHeal/wound-image-uploads"
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DEFAULT_PX_PER_CM = 38.0
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PX_PER_CM_MIN, PX_PER_CM_MAX = 5.0, 1200.0
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# Segmentation preprocessing knobs
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SEG_EXPECTS_RGB = os.getenv("SEG_EXPECTS_RGB", "1") == "1" # most TF models trained on RGB
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SEG_NORM = os.getenv("SEG_NORM", "0to1") # "0to1" | "imagenet"
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SEG_THRESH = float(os.getenv("SEG_THRESH", "0.5"))
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models_cache: Dict[str, object] = {}
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knowledge_base_cache: Dict[str, object] = {}
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# ---------- Utilities to prevent CUDA in main process ----------
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from contextlib import contextmanager
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@contextmanager
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def _no_cuda_env():
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"""
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Mask GPUs so any library imported/constructed in the main process
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cannot see CUDA (required for Spaces Stateless GPU).
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"""
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prev = os.environ.get("CUDA_VISIBLE_DEVICES")
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os.environ["CUDA_VISIBLE_DEVICES"] = "-1"
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try:
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yield
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finally:
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if prev is None:
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os.environ.pop("CUDA_VISIBLE_DEVICES", None)
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else:
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os.environ["CUDA_VISIBLE_DEVICES"] = prev
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# ---------- Lazy imports (wrapped where needed) ----------
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def _import_ultralytics():
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# Prevent Ultralytics from probing CUDA on import
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with _no_cuda_env():
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from ultralytics import YOLO
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return YOLO
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def _import_tf_loader():
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import tensorflow as tf
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tf.config.set_visible_devices([], "GPU")
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from tensorflow.keras.models import load_model
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return load_model
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def _import_hf_cls():
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from transformers import pipeline
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return pipeline
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def _import_embeddings():
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from langchain_community.embeddings import HuggingFaceEmbeddings
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return HuggingFaceEmbeddings
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def _import_langchain_pdf():
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from langchain_community.document_loaders import PyPDFLoader
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return PyPDFLoader
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def _import_langchain_faiss():
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from langchain_community.vectorstores import FAISS
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return FAISS
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def _import_hf_hub():
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from huggingface_hub import HfApi, HfFolder
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return HfApi, HfFolder
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# ---------- SmartHeal prompts (system + user prefix) ----------
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SMARTHEAL_SYSTEM_PROMPT = """\
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You are SmartHeal Clinical Assistant, a wound-care decision-support system.
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You analyze wound photographs and brief patient context to produce careful,
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specific, guideline-informed recommendations WITHOUT diagnosing. You always:
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- Use the measurements calculated by the vision pipeline as ground truth.
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- Prefer concise, actionable steps tailored to exudate level, infection risk, and pain.
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- Flag uncertainties and red flags that need escalation to a clinician.
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- Avoid contraindicated advice; do not infer unseen comorbidities.
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- Keep under 300 words and use the requested headings exactly.
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- Tone: professional, clear, and conservative; no definitive medical claims.
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- Safety: remind the user to seek clinician review for changes or red flags.
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"""
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SMARTHEAL_USER_PREFIX = """\
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Patient: {patient_info}
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Visual findings: type={wound_type}, size={length_cm}x{breadth_cm} cm, area={area_cm2} cm^2,
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detection_conf={det_conf:.2f}, calibration={px_per_cm} px/cm.
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Guideline context (snippets you can draw principles from; do not quote at length):
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{guideline_context}
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Write a structured answer with these headings exactly:
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1. Clinical Summary (max 4 bullet points)
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2. Likely Stage/Type (if uncertain, say 'uncertain')
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3. Treatment Plan (specific dressing choices and frequency based on exudate/infection risk)
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4. Red Flags (what to escalate and when)
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5. Follow-up Cadence (days)
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6. Notes (assumptions/uncertainties)
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Keep to 220–300 words. Do NOT provide diagnosis. Avoid contraindicated advice.
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"""
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# ---------- MedGemma-only text generator ----------
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@_SPACES_GPU(enable_queue=True)
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def _medgemma_generate_gpu(prompt: str, model_id: str, max_new_tokens: int, token: Optional[str]):
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"""
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Runs entirely inside a Spaces GPU worker. Uses Med-Gemma (text-only) to draft the report.
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"""
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import torch
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from transformers import pipeline
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pipe = pipeline(
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task="text-generation",
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model=model_id,
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torch_dtype=torch.bfloat16 if torch.cuda.is_available() else torch.float32,
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device_map="auto" if torch.cuda.is_available() else None,
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token=token,
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trust_remote_code=True,
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model_kwargs={"low_cpu_mem_usage": True},
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)
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out = pipe(
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prompt,
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max_new_tokens=max_new_tokens,
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do_sample=False,
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temperature=0.2,
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return_full_text=True,
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)
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text = (out[0].get("generated_text") if isinstance(out, list) else out).strip()
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# Remove the prompt echo if present
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if text.startswith(prompt):
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text = text[len(prompt):].lstrip()
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return text or "⚠️ Empty response"
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def generate_medgemma_report( # kept name so callers don't change
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patient_info: str,
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visual_results: Dict,
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guideline_context: str,
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image_pil: Image.Image, # kept for signature compatibility; not used by MedGemma
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max_new_tokens: Optional[int] = None,
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) -> str:
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"""
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MedGemma (text-only) report generation.
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The image is analyzed by the vision pipeline; MedGemma formats clinical guidance text.
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"""
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if os.getenv("SMARTHEAL_ENABLE_VLM", "1") != "1":
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return "⚠️ VLM disabled"
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# Default to a public Med-Gemma instruction-tuned model (update via env if you have access to another).
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model_id = os.getenv("SMARTHEAL_MEDGEMMA_MODEL", "google/med-gemma-2-2b-it")
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max_new_tokens = max_new_tokens or int(os.getenv("SMARTHEAL_VLM_MAX_TOKENS", "600"))
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uprompt = SMARTHEAL_USER_PREFIX.format(
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patient_info=patient_info,
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wound_type=visual_results.get("wound_type", "Unknown"),
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length_cm=visual_results.get("length_cm", 0),
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breadth_cm=visual_results.get("breadth_cm", 0),
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area_cm2=visual_results.get("surface_area_cm2", 0),
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det_conf=float(visual_results.get("detection_confidence", 0.0)),
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px_per_cm=visual_results.get("px_per_cm", "?"),
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guideline_context=(guideline_context or "")[:900],
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)
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# Compose a single text prompt
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prompt = f"{SMARTHEAL_SYSTEM_PROMPT}\n\n{uprompt}\n\nAnswer:"
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try:
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return _medgemma_generate_gpu(prompt, model_id, max_new_tokens, HF_TOKEN)
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except Exception as e:
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logging.error(f"MedGemma call failed: {e}")
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return "⚠️ VLM error"
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# ---------- Input-shape helpers (avoid `.as_list()` on strings) ----------
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def _shape_to_hw(shape) -> Tuple[Optional[int], Optional[int]]:
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try:
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if hasattr(shape, "as_list"):
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shape = shape.as_list()
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except Exception:
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pass
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if isinstance(shape, (tuple, list)):
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if len(shape) == 4: # (None, H, W, C)
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H, W = shape[1], shape[2]
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elif len(shape) == 3: # (H, W, C)
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H, W = shape[0], shape[1]
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else:
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return (None, None)
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try: H = int(H) if (H is not None and str(H).lower() != "none") else None
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except Exception: H = None
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try: W = int(W) if (W is not None and str(W).lower() != "none") else None
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except Exception: W = None
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return (H, W)
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return (None, None)
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def _get_model_input_hw(model, default_hw: Tuple[int, int] = (224, 224)) -> Tuple[int, int]:
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H, W = _shape_to_hw(getattr(model, "input_shape", None))
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if H and W:
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return H, W
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try:
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inputs = getattr(model, "inputs", None)
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if inputs:
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H, W = _shape_to_hw(inputs[0].shape)
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if H and W:
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return H, W
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except Exception:
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pass
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try:
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cfg = model.get_config() if hasattr(model, "get_config") else None
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if isinstance(cfg, dict):
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for layer in cfg.get("layers", []):
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conf = (layer or {}).get("config", {})
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cand = conf.get("batch_input_shape") or conf.get("batch_shape")
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H, W = _shape_to_hw(cand)
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if H and W:
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return H, W
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except Exception:
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pass
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logging.warning(f"Could not resolve model input shape; using default {default_hw}.")
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return default_hw
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# ---------- Initialize CPU models ----------
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def load_yolo_model():
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YOLO = _import_ultralytics()
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with _no_cuda_env():
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model = YOLO(YOLO_MODEL_PATH)
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return model
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def load_segmentation_model(path: Optional[str] = None):
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"""
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Robust loader for legacy .h5 models across TF/Keras versions.
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Uses global SEG_MODEL_PATH by default.
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"""
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import ast
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import tensorflow as tf
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tf.config.set_visible_devices([], "GPU")
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model_path = path or SEG_MODEL_PATH
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# Attempt 1: tf.keras with safe_mode=False
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try:
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m = tf.keras.models.load_model(model_path, compile=False, safe_mode=False)
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logging.info("✅ Segmentation model loaded (tf.keras, safe_mode=False).")
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return m
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except Exception as e1:
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logging.warning(f"tf.keras load (safe_mode=False) failed: {e1}")
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# Attempt 2: patched InputLayer (drop legacy args; coerce string shapes)
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try:
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from tensorflow.keras.layers import InputLayer as _KInputLayer
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def _InputLayerPatched(*args, **kwargs):
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kwargs.pop("batch_shape", None)
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kwargs.pop("batch_input_shape", None)
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if "shape" in kwargs and isinstance(kwargs["shape"], str):
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try:
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kwargs["shape"] = tuple(ast.literal_eval(kwargs["shape"]))
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except Exception:
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kwargs.pop("shape", None)
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return _KInputLayer(**kwargs)
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m = tf.keras.models.load_model(
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model_path,
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compile=False,
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custom_objects={"InputLayer": _InputLayerPatched},
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safe_mode=False,
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)
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logging.info("✅ Segmentation model loaded (patched InputLayer).")
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return m
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except Exception as e2:
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logging.warning(f"Patched InputLayer load failed: {e2}")
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# Attempt 3: keras 2 shim (tf_keras) if present
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try:
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import tf_keras
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m = tf_keras.models.load_model(model_path, compile=False)
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logging.info("✅ Segmentation model loaded (tf_keras compat).")
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return m
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except Exception as e3:
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logging.warning(f"tf_keras load failed or not installed: {e3}")
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raise RuntimeError("Segmentation model could not be loaded; please convert/resave the model.")
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def load_classification_pipeline():
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pipe = _import_hf_cls()
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return pipe("image-classification", model="Hemg/Wound-classification", token=HF_TOKEN, device="cpu")
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def load_embedding_model():
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Emb = _import_embeddings()
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return Emb(model_name="sentence-transformers/all-MiniLM-L6-v2", model_kwargs={"device": "cpu"})
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def initialize_cpu_models() -> None:
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if HF_TOKEN:
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try:
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HfApi, HfFolder = _import_hf_hub()
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HfFolder.save_token(HF_TOKEN)
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logging.info("✅ HF token set")
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except Exception as e:
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logging.warning(f"HF token save failed: {e}")
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if "det" not in models_cache:
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try:
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models_cache["det"] = load_yolo_model()
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logging.info("✅ YOLO loaded (CPU; CUDA masked in main)")
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except Exception as e:
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logging.error(f"YOLO load failed: {e}")
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if "seg" not in models_cache:
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try:
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if os.path.exists(SEG_MODEL_PATH):
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m = load_segmentation_model() # uses global path by default
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models_cache["seg"] = m
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th, tw = _get_model_input_hw(m, default_hw=(224, 224))
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oshape = getattr(m, "output_shape", None)
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logging.info(f"✅ Segmentation model loaded (CPU) | input_hw=({th},{tw}) output_shape={oshape}")
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else:
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models_cache["seg"] = None
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logging.warning("Segmentation model file missing; skipping.")
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except Exception as e:
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models_cache["seg"] = None
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logging.warning(f"Segmentation unavailable: {e}")
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if "cls" not in models_cache:
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try:
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models_cache["cls"] = load_classification_pipeline()
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logging.info("✅ Classifier loaded (CPU)")
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except Exception as e:
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models_cache["cls"] = None
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logging.warning(f"Classifier unavailable: {e}")
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|
| 360 |
-
if "embedding_model" not in models_cache:
|
| 361 |
-
try:
|
| 362 |
-
models_cache["embedding_model"] = load_embedding_model()
|
| 363 |
-
logging.info("✅ Embeddings loaded (CPU)")
|
| 364 |
-
except Exception as e:
|
| 365 |
-
models_cache["embedding_model"] = None
|
| 366 |
-
logging.warning(f"Embeddings unavailable: {e}")
|
| 367 |
-
|
| 368 |
-
def setup_knowledge_base() -> None:
|
| 369 |
-
if "vector_store" in knowledge_base_cache:
|
| 370 |
-
return
|
| 371 |
-
docs: List = []
|
| 372 |
-
try:
|
| 373 |
-
PyPDFLoader = _import_langchain_pdf()
|
| 374 |
-
for pdf in GUIDELINE_PDFS:
|
| 375 |
-
if os.path.exists(pdf):
|
| 376 |
-
try:
|
| 377 |
-
docs.extend(PyPDFLoader(pdf).load())
|
| 378 |
-
logging.info(f"Loaded PDF: {pdf}")
|
| 379 |
-
except Exception as e:
|
| 380 |
-
logging.warning(f"PDF load failed ({pdf}): {e}")
|
| 381 |
-
except Exception as e:
|
| 382 |
-
logging.warning(f"LangChain PDF loader unavailable: {e}")
|
| 383 |
-
|
| 384 |
-
if docs and models_cache.get("embedding_model"):
|
| 385 |
-
try:
|
| 386 |
-
from langchain.text_splitter import RecursiveCharacterTextSplitter
|
| 387 |
-
FAISS = _import_langchain_faiss()
|
| 388 |
-
chunks = RecursiveCharacterTextSplitter(chunk_size=1000, chunk_overlap=100).split_documents(docs)
|
| 389 |
-
knowledge_base_cache["vector_store"] = FAISS.from_documents(chunks, models_cache["embedding_model"])
|
| 390 |
-
logging.info(f"✅ Knowledge base ready ({len(chunks)} chunks)")
|
| 391 |
-
except Exception as e:
|
| 392 |
-
knowledge_base_cache["vector_store"] = None
|
| 393 |
-
logging.warning(f"KB build failed: {e}")
|
| 394 |
-
else:
|
| 395 |
-
knowledge_base_cache["vector_store"] = None
|
| 396 |
-
logging.warning("KB disabled (no docs or embeddings).")
|
| 397 |
-
|
| 398 |
-
initialize_cpu_models()
|
| 399 |
-
setup_knowledge_base()
|
| 400 |
-
|
| 401 |
-
# ---------- Calibration helpers ----------
|
| 402 |
-
def _exif_to_dict(pil_img: Image.Image) -> Dict[str, object]:
|
| 403 |
-
out = {}
|
| 404 |
-
try:
|
| 405 |
-
exif = pil_img.getexif()
|
| 406 |
-
if not exif:
|
| 407 |
-
return out
|
| 408 |
-
for k, v in exif.items():
|
| 409 |
-
tag = TAGS.get(k, k)
|
| 410 |
-
out[tag] = v
|
| 411 |
-
except Exception:
|
| 412 |
-
pass
|
| 413 |
-
return out
|
| 414 |
-
|
| 415 |
-
def _to_float(val) -> Optional[float]:
|
| 416 |
-
try:
|
| 417 |
-
if val is None:
|
| 418 |
-
return None
|
| 419 |
-
if isinstance(val, tuple) and len(val) == 2:
|
| 420 |
-
num, den = float(val[0]), float(val[1]) if float(val[1]) != 0 else 1.0
|
| 421 |
-
return num / den
|
| 422 |
-
return float(val)
|
| 423 |
-
except Exception:
|
| 424 |
-
return None
|
| 425 |
-
|
| 426 |
-
def _estimate_sensor_width_mm(f_mm: Optional[float], f35: Optional[float]) -> Optional[float]:
|
| 427 |
-
if f_mm and f35 and f35 > 0:
|
| 428 |
-
return 36.0 * f_mm / f35
|
| 429 |
-
return None
|
| 430 |
-
|
| 431 |
-
def estimate_px_per_cm_from_exif(pil_img: Image.Image, default_px_per_cm: float = DEFAULT_PX_PER_CM) -> Tuple[float, Dict]:
|
| 432 |
-
meta = {"used": "default", "f_mm": None, "f35": None, "sensor_w_mm": None, "distance_m": None}
|
| 433 |
-
try:
|
| 434 |
-
exif = _exif_to_dict(pil_img)
|
| 435 |
-
f_mm = _to_float(exif.get("FocalLength"))
|
| 436 |
-
f35 = _to_float(exif.get("FocalLengthIn35mmFilm") or exif.get("FocalLengthIn35mm"))
|
| 437 |
-
subj_dist_m = _to_float(exif.get("SubjectDistance"))
|
| 438 |
-
sensor_w_mm = _estimate_sensor_width_mm(f_mm, f35)
|
| 439 |
-
meta.update({"f_mm": f_mm, "f35": f35, "sensor_w_mm": sensor_w_mm, "distance_m": subj_dist_m})
|
| 440 |
-
|
| 441 |
-
if f_mm and sensor_w_mm and subj_dist_m and subj_dist_m > 0:
|
| 442 |
-
w_px = pil_img.width
|
| 443 |
-
field_w_mm = sensor_w_mm * (subj_dist_m * 1000.0) / f_mm
|
| 444 |
-
field_w_cm = field_w_mm / 10.0
|
| 445 |
-
px_per_cm = w_px / max(field_w_cm, 1e-6)
|
| 446 |
-
px_per_cm = float(np.clip(px_per_cm, PX_PER_CM_MIN, PX_PER_CM_MAX))
|
| 447 |
-
meta["used"] = "exif"
|
| 448 |
-
return px_per_cm, meta
|
| 449 |
-
return float(default_px_per_cm), meta
|
| 450 |
-
except Exception:
|
| 451 |
-
return float(default_px_per_cm), meta
|
| 452 |
-
|
| 453 |
-
# ---------- Segmentation helpers ----------
|
| 454 |
-
def _imagenet_norm(arr: np.ndarray) -> np.ndarray:
|
| 455 |
-
mean = np.array([123.675, 116.28, 103.53], dtype=np.float32)
|
| 456 |
-
std = np.array([58.395, 57.12, 57.375], dtype=np.float32)
|
| 457 |
-
return (arr.astype(np.float32) - mean) / std
|
| 458 |
-
|
| 459 |
-
def _preprocess_for_seg(bgr_roi: np.ndarray, target_hw: Tuple[int, int]) -> np.ndarray:
|
| 460 |
-
H, W = target_hw
|
| 461 |
-
resized = cv2.resize(bgr_roi, (W, H), interpolation=cv2.INTER_LINEAR)
|
| 462 |
-
if SEG_EXPECTS_RGB:
|
| 463 |
-
resized = cv2.cvtColor(resized, cv2.COLOR_BGR2RGB)
|
| 464 |
-
if SEG_NORM.lower() == "imagenet":
|
| 465 |
-
x = _imagenet_norm(resized)
|
| 466 |
-
else:
|
| 467 |
-
x = resized.astype(np.float32) / 255.0
|
| 468 |
-
x = np.expand_dims(x, axis=0) # (1,H,W,3)
|
| 469 |
-
return x
|
| 470 |
-
|
| 471 |
-
def _to_prob(pred: np.ndarray) -> np.ndarray:
|
| 472 |
-
p = np.squeeze(pred)
|
| 473 |
-
pmin, pmax = float(p.min()), float(p.max())
|
| 474 |
-
if pmax > 1.0 or pmin < 0.0:
|
| 475 |
-
p = 1.0 / (1.0 + np.exp(-p))
|
| 476 |
-
return p.astype(np.float32)
|
| 477 |
-
|
| 478 |
-
# ---- Adaptive threshold + GrabCut grow ----
|
| 479 |
-
def _adaptive_prob_threshold(p: np.ndarray) -> float:
|
| 480 |
-
"""
|
| 481 |
-
Choose a threshold that avoids tiny blobs while not swallowing skin.
|
| 482 |
-
Try Otsu and the 90th percentile, clamp to [0.25, 0.65], pick by area heuristic.
|
| 483 |
-
"""
|
| 484 |
-
p01 = np.clip(p.astype(np.float32), 0, 1)
|
| 485 |
-
p255 = (p01 * 255).astype(np.uint8)
|
| 486 |
-
|
| 487 |
-
ret_otsu, _ = cv2.threshold(p255, 0, 255, cv2.THRESH_BINARY + cv2.THRESH_OTSU)
|
| 488 |
-
thr_otsu = float(np.clip(ret_otsu / 255.0, 0.25, 0.65))
|
| 489 |
-
thr_pctl = float(np.clip(np.percentile(p01, 90), 0.25, 0.65))
|
| 490 |
-
|
| 491 |
-
def area_frac(thr: float) -> float:
|
| 492 |
-
return float((p01 >= thr).sum()) / float(p01.size)
|
| 493 |
-
|
| 494 |
-
af_otsu = area_frac(thr_otsu)
|
| 495 |
-
af_pctl = area_frac(thr_pctl)
|
| 496 |
-
|
| 497 |
-
def score(af: float) -> float:
|
| 498 |
-
target_low, target_high = 0.03, 0.10
|
| 499 |
-
if af < target_low: return abs(af - target_low) * 3.0
|
| 500 |
-
if af > target_high: return abs(af - target_high) * 1.5
|
| 501 |
-
return 0.0
|
| 502 |
-
|
| 503 |
-
return thr_otsu if score(af_otsu) <= score(af_pctl) else thr_pctl
|
| 504 |
-
|
| 505 |
-
def _grabcut_refine(bgr: np.ndarray, seed01: np.ndarray, iters: int = 3) -> np.ndarray:
|
| 506 |
-
"""Grow from a confident core into low-contrast margins."""
|
| 507 |
-
h, w = bgr.shape[:2]
|
| 508 |
-
gc = np.full((h, w), cv2.GC_PR_BGD, np.uint8)
|
| 509 |
-
k = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (5, 5))
|
| 510 |
-
seed_dil = cv2.dilate(seed01, k, iterations=1)
|
| 511 |
-
gc[seed01.astype(bool)] = cv2.GC_PR_FGD
|
| 512 |
-
gc[seed_dil.astype(bool)] = cv2.GC_FGD
|
| 513 |
-
gc[0, :], gc[-1, :], gc[:, 0], gc[:, 1] = cv2.GC_BGD, cv2.GC_BGD, cv2.GC_BGD, cv2.GC_BGD
|
| 514 |
-
bgdModel = np.zeros((1, 65), np.float64)
|
| 515 |
-
fgdModel = np.zeros((1, 65), np.float64)
|
| 516 |
-
cv2.grabCut(bgr, gc, None, bgdModel, fgdModel, iters, cv2.GC_INIT_WITH_MASK)
|
| 517 |
-
return np.where((gc == cv2.GC_FGD) | (gc == cv2.GC_PR_FGD), 1, 0).astype(np.uint8)
|
| 518 |
-
|
| 519 |
-
def _fill_holes(mask01: np.ndarray) -> np.ndarray:
|
| 520 |
-
h, w = mask01.shape[:2]
|
| 521 |
-
ff = np.zeros((h + 2, w + 2), np.uint8)
|
| 522 |
-
m = (mask01 * 255).astype(np.uint8).copy()
|
| 523 |
-
cv2.floodFill(m, ff, (0, 0), 255)
|
| 524 |
-
m_inv = cv2.bitwise_not(m)
|
| 525 |
-
out = ((mask01 * 255) | m_inv) // 255
|
| 526 |
-
return out.astype(np.uint8)
|
| 527 |
-
|
| 528 |
-
def _clean_mask(mask01: np.ndarray) -> np.ndarray:
|
| 529 |
-
"""Open → Close → Fill holes → Largest component (no dilation)."""
|
| 530 |
-
mask01 = (mask01 > 0).astype(np.uint8)
|
| 531 |
-
k3 = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (3, 3))
|
| 532 |
-
k5 = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (5, 5))
|
| 533 |
-
mask01 = cv2.morphologyEx(mask01, cv2.MORPH_OPEN, k3, iterations=1)
|
| 534 |
-
mask01 = cv2.morphologyEx(mask01, cv2.MORPH_CLOSE, k5, iterations=1)
|
| 535 |
-
mask01 = _fill_holes(mask01)
|
| 536 |
-
# Keep largest component only
|
| 537 |
-
num, labels, stats, _ = cv2.connectedComponentsWithStats(mask01, 8)
|
| 538 |
-
if num > 1:
|
| 539 |
-
areas = stats[1:, cv2.CC_STAT_AREA]
|
| 540 |
-
if areas.size:
|
| 541 |
-
largest_idx = 1 + int(np.argmax(areas))
|
| 542 |
-
mask01 = (labels == largest_idx).astype(np.uint8)
|
| 543 |
-
return (mask01 > 0).astype(np.uint8)
|
| 544 |
-
|
| 545 |
-
# Global last debug dict (per-process)
|
| 546 |
-
_last_seg_debug: Dict[str, object] = {}
|
| 547 |
-
|
| 548 |
-
def segment_wound(image_bgr: np.ndarray, ts: str, out_dir: str) -> Tuple[np.ndarray, Dict[str, object]]:
|
| 549 |
-
"""
|
| 550 |
-
TF model → adaptive threshold on prob → GrabCut grow → cleanup.
|
| 551 |
-
Fallback: KMeans-Lab.
|
| 552 |
-
Returns (mask_uint8_0_255, debug_dict)
|
| 553 |
-
"""
|
| 554 |
-
debug = {"used": None, "reason": None, "positive_fraction": 0.0,
|
| 555 |
-
"thr": None, "heatmap_path": None, "roi_seen_by_model": None}
|
| 556 |
-
|
| 557 |
-
seg_model = models_cache.get("seg", None)
|
| 558 |
-
|
| 559 |
-
# --- Model path ---
|
| 560 |
-
if seg_model is not None:
|
| 561 |
-
try:
|
| 562 |
-
th, tw = _get_model_input_hw(seg_model, default_hw=(224, 224))
|
| 563 |
-
x = _preprocess_for_seg(image_bgr, (th, tw))
|
| 564 |
-
roi_seen_path = None
|
| 565 |
-
if SMARTHEAL_DEBUG:
|
| 566 |
-
roi_seen_path = os.path.join(out_dir, f"roi_for_seg_{ts}.png")
|
| 567 |
-
cv2.imwrite(roi_seen_path, image_bgr)
|
| 568 |
-
|
| 569 |
-
pred = seg_model.predict(x, verbose=0)
|
| 570 |
-
if isinstance(pred, (list, tuple)): pred = pred[0]
|
| 571 |
-
p = _to_prob(pred)
|
| 572 |
-
p = cv2.resize(p, (image_bgr.shape[1], image_bgr.shape[0]), interpolation=cv2.INTER_LINEAR)
|
| 573 |
-
|
| 574 |
-
heatmap_path = None
|
| 575 |
-
if SMARTHEAL_DEBUG:
|
| 576 |
-
hm = (np.clip(p, 0, 1) * 255).astype(np.uint8)
|
| 577 |
-
heat = cv2.applyColorMap(hm, cv2.COLORMAP_JET)
|
| 578 |
-
heatmap_path = os.path.join(out_dir, f"seg_pred_heatmap_{ts}.png")
|
| 579 |
-
cv2.imwrite(heatmap_path, heat)
|
| 580 |
-
|
| 581 |
-
thr = _adaptive_prob_threshold(p)
|
| 582 |
-
core01 = (p >= thr).astype(np.uint8)
|
| 583 |
-
core_frac = float(core01.sum()) / float(core01.size)
|
| 584 |
-
|
| 585 |
-
if core_frac < 0.005:
|
| 586 |
-
thr2 = max(thr - 0.10, 0.15)
|
| 587 |
-
core01 = (p >= thr2).astype(np.uint8)
|
| 588 |
-
thr = thr2
|
| 589 |
-
core_frac = float(core01.sum()) / float(core01.size)
|
| 590 |
-
|
| 591 |
-
if core01.any():
|
| 592 |
-
gc01 = _grabcut_refine(image_bgr, core01, iters=3)
|
| 593 |
-
mask01 = _clean_mask(gc01)
|
| 594 |
-
else:
|
| 595 |
-
mask01 = np.zeros(core01.shape, np.uint8)
|
| 596 |
-
|
| 597 |
-
pos_frac = float(mask01.sum()) / float(mask01.size)
|
| 598 |
-
logging.info(f"SegModel USED | thr={float(thr):.2f} core_frac={core_frac:.4f} final_frac={pos_frac:.4f}")
|
| 599 |
-
|
| 600 |
-
debug.update({
|
| 601 |
-
"used": "tf_model",
|
| 602 |
-
"reason": "ok",
|
| 603 |
-
"positive_fraction": pos_frac,
|
| 604 |
-
"thr": float(thr),
|
| 605 |
-
"heatmap_path": heatmap_path,
|
| 606 |
-
"roi_seen_by_model": roi_seen_path
|
| 607 |
-
})
|
| 608 |
-
return (mask01 * 255).astype(np.uint8), debug
|
| 609 |
-
|
| 610 |
-
except Exception as e:
|
| 611 |
-
logging.warning(f"⚠️ Segmentation model failed → fallback. Reason: {e}")
|
| 612 |
-
debug.update({"used": "fallback_kmeans", "reason": f"model_failed: {e}"})
|
| 613 |
-
|
| 614 |
-
# --- Fallback: KMeans in Lab (reddest cluster as wound) ---
|
| 615 |
-
Z = image_bgr.reshape((-1, 3)).astype(np.float32)
|
| 616 |
-
criteria = (cv2.TERM_CRITERIA_EPS + cv2.TERM_CRITERIA_MAX_ITER, 10, 1.0)
|
| 617 |
-
_, labels, centers = cv2.kmeans(Z, 2, None, criteria, 5, cv2.KMEANS_PP_CENTERS)
|
| 618 |
-
centers_u8 = centers.astype(np.uint8).reshape(1, 2, 3)
|
| 619 |
-
centers_lab = cv2.cvtColor(centers_u8, cv2.COLOR_BGR2LAB)[0]
|
| 620 |
-
wound_idx = int(np.argmax(centers_lab[:, 1])) # maximize a* (red)
|
| 621 |
-
mask01 = (labels.reshape(image_bgr.shape[:2]) == wound_idx).astype(np.uint8)
|
| 622 |
-
mask01 = _clean_mask(mask01)
|
| 623 |
-
|
| 624 |
-
pos_frac = float(mask01.sum()) / float(mask01.size)
|
| 625 |
-
logging.info(f"KMeans USED | final_frac={pos_frac:.4f}")
|
| 626 |
-
|
| 627 |
-
debug.update({
|
| 628 |
-
"used": "fallback_kmeans",
|
| 629 |
-
"reason": debug.get("reason") or "no_model",
|
| 630 |
-
"positive_fraction": pos_frac,
|
| 631 |
-
"thr": None
|
| 632 |
-
})
|
| 633 |
-
return (mask01 * 255).astype(np.uint8), debug
|
| 634 |
-
|
| 635 |
-
# ---------- Measurement + overlay helpers ----------
|
| 636 |
-
def largest_component_mask(binary01: np.ndarray, min_area_px: int = 50) -> np.ndarray:
|
| 637 |
-
num, labels, stats, _ = cv2.connectedComponentsWithStats(binary01.astype(np.uint8), connectivity=8)
|
| 638 |
-
if num <= 1:
|
| 639 |
-
return binary01.astype(np.uint8)
|
| 640 |
-
areas = stats[1:, cv2.CC_STAT_AREA]
|
| 641 |
-
if areas.size == 0 or areas.max() < min_area_px:
|
| 642 |
-
return binary01.astype(np.uint8)
|
| 643 |
-
largest_idx = 1 + int(np.argmax(areas))
|
| 644 |
-
return (labels == largest_idx).astype(np.uint8)
|
| 645 |
-
|
| 646 |
-
def measure_min_area_rect(mask01: np.ndarray, px_per_cm: float) -> Tuple[float, float, Tuple]:
|
| 647 |
-
contours, _ = cv2.findContours(mask01.astype(np.uint8), cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
|
| 648 |
-
if not contours:
|
| 649 |
-
return 0.0, 0.0, (None, None)
|
| 650 |
-
cnt = max(contours, key=cv2.contourArea)
|
| 651 |
-
rect = cv2.minAreaRect(cnt)
|
| 652 |
-
(w_px, h_px) = rect[1]
|
| 653 |
-
length_px, breadth_px = (max(w_px, h_px), min(h_px, w_px))
|
| 654 |
-
length_cm = round(length_px / max(px_per_cm, 1e-6), 2)
|
| 655 |
-
breadth_cm = round(breadth_px / max(px_per_cm, 1e-6), 2)
|
| 656 |
-
box = cv2.boxPoints(rect).astype(int)
|
| 657 |
-
return length_cm, breadth_cm, (box, rect[0])
|
| 658 |
-
|
| 659 |
-
def area_cm2_from_contour(mask01: np.ndarray, px_per_cm: float) -> Tuple[float, Optional[np.ndarray]]:
|
| 660 |
-
"""Area from largest polygon (sub-pixel); returns (area_cm2, contour)."""
|
| 661 |
-
m = (mask01 > 0).astype(np.uint8)
|
| 662 |
-
contours, _ = cv2.findContours(m, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
|
| 663 |
-
if not contours:
|
| 664 |
-
return 0.0, None
|
| 665 |
-
cnt = max(contours, key=cv2.contourArea)
|
| 666 |
-
poly_area_px2 = float(cv2.contourArea(cnt))
|
| 667 |
-
area_cm2 = round(poly_area_px2 / (max(px_per_cm, 1e-6) ** 2), 2)
|
| 668 |
-
return area_cm2, cnt
|
| 669 |
-
|
| 670 |
-
def clamp_area_with_minrect(cnt: np.ndarray, px_per_cm: float, area_cm2_poly: float) -> float:
|
| 671 |
-
rect = cv2.minAreaRect(cnt)
|
| 672 |
-
(w_px, h_px) = rect[1]
|
| 673 |
-
rect_area_px2 = float(max(w_px, 0.0) * max(h_px, 0.0))
|
| 674 |
-
rect_area_cm2 = rect_area_px2 / (max(px_per_cm, 1e-6) ** 2)
|
| 675 |
-
return round(min(area_cm2_poly, rect_area_cm2 * 1.05), 2)
|
| 676 |
-
|
| 677 |
-
def draw_measurement_overlay(
|
| 678 |
-
base_bgr: np.ndarray,
|
| 679 |
-
mask01: np.ndarray,
|
| 680 |
-
rect_box: np.ndarray,
|
| 681 |
-
length_cm: float,
|
| 682 |
-
breadth_cm: float,
|
| 683 |
-
thickness: int = 2
|
| 684 |
-
) -> np.ndarray:
|
| 685 |
-
"""
|
| 686 |
-
1) Strong red mask overlay + white contour
|
| 687 |
-
2) Min-area rectangle
|
| 688 |
-
3) Double-headed arrows labeled Length/Width
|
| 689 |
-
"""
|
| 690 |
-
overlay = base_bgr.copy()
|
| 691 |
-
|
| 692 |
-
# Mask tint
|
| 693 |
-
mask255 = (mask01 * 255).astype(np.uint8)
|
| 694 |
-
mask3 = cv2.merge([mask255, mask255, mask255])
|
| 695 |
-
red = np.zeros_like(overlay); red[:] = (0, 0, 255)
|
| 696 |
-
alpha = 0.55
|
| 697 |
-
tinted = cv2.addWeighted(overlay, 1 - alpha, red, alpha, 0)
|
| 698 |
-
overlay = np.where(mask3 > 0, tinted, overlay)
|
| 699 |
-
|
| 700 |
-
# Contour
|
| 701 |
-
cnts, _ = cv2.findContours(mask255, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
|
| 702 |
-
if cnts:
|
| 703 |
-
cv2.drawContours(overlay, cnts, -1, (255, 255, 255), 2)
|
| 704 |
-
|
| 705 |
-
if rect_box is not None:
|
| 706 |
-
cv2.polylines(overlay, [rect_box], True, (255, 255, 255), thickness)
|
| 707 |
-
pts = rect_box.reshape(-1, 2)
|
| 708 |
-
|
| 709 |
-
def midpoint(a, b): return (int((a[0] + b[0]) / 2), int((a[1] + b[1]) / 2))
|
| 710 |
-
e = [np.linalg.norm(pts[i] - pts[(i + 1) % 4]) for i in range(4)]
|
| 711 |
-
long_edge_idx = int(np.argmax(e))
|
| 712 |
-
mids = [midpoint(pts[i], pts[(i + 1) % 4]) for i in range(4)]
|
| 713 |
-
long_pair = (long_edge_idx, (long_edge_idx + 2) % 4)
|
| 714 |
-
short_pair = ((long_edge_idx + 1) % 4, (long_edge_idx + 3) % 4)
|
| 715 |
-
|
| 716 |
-
def draw_double_arrow(img, p1, p2):
|
| 717 |
-
cv2.arrowedLine(img, p1, p2, (0, 0, 0), thickness + 2, tipLength=0.05)
|
| 718 |
-
cv2.arrowedLine(img, p2, p1, (0, 0, 0), thickness + 2, tipLength=0.05)
|
| 719 |
-
cv2.arrowedLine(img, p1, p2, (255, 255, 255), thickness, tipLength=0.05)
|
| 720 |
-
cv2.arrowedLine(img, p2, p1, (255, 255, 255), thickness, tipLength=0.05)
|
| 721 |
-
|
| 722 |
-
def put_label(text, anchor):
|
| 723 |
-
org = (anchor[0] + 6, anchor[1] - 6)
|
| 724 |
-
cv2.putText(overlay, text, org, cv2.FONT_HERSHEY_SIMPLEX, 0.7, (0, 0, 0), 4, cv2.LINE_AA)
|
| 725 |
-
cv2.putText(overlay, text, org, cv2.FONT_HERSHEY_SIMPLEX, 0.7, (255, 255, 255), 2, cv2.LINE_AA)
|
| 726 |
-
|
| 727 |
-
draw_double_arrow(overlay, mids[long_pair[0]], mids[long_pair[1]])
|
| 728 |
-
draw_double_arrow(overlay, mids[short_pair[0]], mids[short_pair[1]])
|
| 729 |
-
put_label(f"Length: {length_cm:.2f} cm", mids[long_pair[0]])
|
| 730 |
-
put_label(f"Width: {breadth_cm:.2f} cm", mids[short_pair[0]])
|
| 731 |
-
|
| 732 |
-
return overlay
|
| 733 |
-
|
| 734 |
-
# ---------- AI PROCESSOR ----------
|
| 735 |
-
class AIProcessor:
|
| 736 |
def __init__(self):
|
| 737 |
-
self.
|
| 738 |
-
|
| 739 |
-
|
| 740 |
-
|
| 741 |
-
|
| 742 |
-
|
| 743 |
-
|
| 744 |
-
|
| 745 |
-
|
| 746 |
-
|
| 747 |
-
|
| 748 |
-
def perform_visual_analysis(self, image_pil: Image.Image) -> Dict:
|
| 749 |
-
"""
|
| 750 |
-
YOLO detect → crop ROI → segment_wound(ROI) → clean mask →
|
| 751 |
-
minAreaRect measurement (cm) using EXIF px/cm → save outputs.
|
| 752 |
-
"""
|
| 753 |
-
try:
|
| 754 |
-
px_per_cm, exif_meta = estimate_px_per_cm_from_exif(image_pil, DEFAULT_PX_PER_CM)
|
| 755 |
-
# Guardrails for calibration to avoid huge area blow-ups
|
| 756 |
-
px_per_cm = float(np.clip(px_per_cm, 20.0, 350.0))
|
| 757 |
-
if (exif_meta or {}).get("used") != "exif":
|
| 758 |
-
logging.warning(f"Calibration fallback used: px_per_cm={px_per_cm:.2f} (default). Prefer ruler/Aruco for accuracy.")
|
| 759 |
-
|
| 760 |
-
image_cv = cv2.cvtColor(np.array(image_pil.convert("RGB")), cv2.COLOR_RGB2BGR)
|
| 761 |
-
|
| 762 |
-
# --- Detection ---
|
| 763 |
-
det_model = self.models_cache.get("det")
|
| 764 |
-
if det_model is None:
|
| 765 |
-
raise RuntimeError("YOLO model not loaded")
|
| 766 |
-
# Force CPU inference and avoid CUDA touch
|
| 767 |
-
results = det_model.predict(image_cv, verbose=False, device="cpu")
|
| 768 |
-
if (not results) or (not getattr(results[0], "boxes", None)) or (len(results[0].boxes) == 0):
|
| 769 |
-
try:
|
| 770 |
-
import gradio as gr
|
| 771 |
-
raise gr.Error("No wound could be detected.")
|
| 772 |
-
except Exception:
|
| 773 |
-
raise RuntimeError("No wound could be detected.")
|
| 774 |
-
|
| 775 |
-
box = results[0].boxes[0].xyxy[0].cpu().numpy().astype(int)
|
| 776 |
-
x1, y1, x2, y2 = [int(v) for v in box]
|
| 777 |
-
x1, y1 = max(0, x1), max(0, y1)
|
| 778 |
-
x2, y2 = min(image_cv.shape[1], x2), min(image_cv.shape[0], y2)
|
| 779 |
-
roi = image_cv[y1:y2, x1:x2].copy()
|
| 780 |
-
if roi.size == 0:
|
| 781 |
-
try:
|
| 782 |
-
import gradio as gr
|
| 783 |
-
raise gr.Error("Detected ROI is empty.")
|
| 784 |
-
except Exception:
|
| 785 |
-
raise RuntimeError("Detected ROI is empty.")
|
| 786 |
-
|
| 787 |
-
out_dir = self._ensure_analysis_dir()
|
| 788 |
-
ts = datetime.now().strftime("%Y%m%d_%H%M%S")
|
| 789 |
-
|
| 790 |
-
# --- Segmentation (model-first + KMeans fallback) ---
|
| 791 |
-
mask_u8_255, seg_debug = segment_wound(roi, ts, out_dir)
|
| 792 |
-
mask01 = (mask_u8_255 > 127).astype(np.uint8)
|
| 793 |
-
|
| 794 |
-
if mask01.any():
|
| 795 |
-
mask01 = _clean_mask(mask01)
|
| 796 |
-
logging.debug(f"Mask postproc: px_after={int(mask01.sum())}")
|
| 797 |
-
|
| 798 |
-
# --- Measurement (accurate & conservative) ---
|
| 799 |
-
if mask01.any():
|
| 800 |
-
length_cm, breadth_cm, (box_pts, _) = measure_min_area_rect(mask01, px_per_cm)
|
| 801 |
-
area_poly_cm2, largest_cnt = area_cm2_from_contour(mask01, px_per_cm)
|
| 802 |
-
if largest_cnt is not None:
|
| 803 |
-
surface_area_cm2 = clamp_area_with_minrect(largest_cnt, px_per_cm, area_poly_cm2)
|
| 804 |
-
else:
|
| 805 |
-
surface_area_cm2 = area_poly_cm2
|
| 806 |
-
|
| 807 |
-
anno_roi = draw_measurement_overlay(roi, mask01, box_pts, length_cm, breadth_cm)
|
| 808 |
-
segmentation_empty = False
|
| 809 |
-
else:
|
| 810 |
-
# Fallback if seg failed: use ROI dimensions
|
| 811 |
-
h_px = max(0, y2 - y1); w_px = max(0, x2 - x1)
|
| 812 |
-
length_cm = round(max(h_px, w_px) / px_per_cm, 2)
|
| 813 |
-
breadth_cm = round(min(h_px, w_px) / px_per_cm, 2)
|
| 814 |
-
surface_area_cm2 = round((h_px * w_px) / (px_per_cm ** 2), 2)
|
| 815 |
-
anno_roi = roi.copy()
|
| 816 |
-
cv2.rectangle(anno_roi, (2, 2), (anno_roi.shape[1]-3, anno_roi.shape[0]-3), (0, 0, 255), 3)
|
| 817 |
-
cv2.line(anno_roi, (0, 0), (anno_roi.shape[1]-1, anno_roi.shape[0]-1), (0, 0, 255), 2)
|
| 818 |
-
cv2.line(anno_roi, (anno_roi.shape[1]-1, 0), (0, anno_roi.shape[0]-1), (0, 0, 255), 2)
|
| 819 |
-
box_pts = None
|
| 820 |
-
segmentation_empty = True
|
| 821 |
-
|
| 822 |
-
# --- Save visualizations ---
|
| 823 |
-
original_path = os.path.join(out_dir, f"original_{ts}.png")
|
| 824 |
-
cv2.imwrite(original_path, image_cv)
|
| 825 |
-
|
| 826 |
-
det_vis = image_cv.copy()
|
| 827 |
-
cv2.rectangle(det_vis, (x1, y1), (x2, y2), (0, 255, 0), 2)
|
| 828 |
-
detection_path = os.path.join(out_dir, f"detection_{ts}.png")
|
| 829 |
-
cv2.imwrite(detection_path, det_vis)
|
| 830 |
-
|
| 831 |
-
roi_mask_path = os.path.join(out_dir, f"roi_mask_{ts}.png")
|
| 832 |
-
cv2.imwrite(roi_mask_path, (mask01 * 255).astype(np.uint8))
|
| 833 |
-
|
| 834 |
-
# ROI overlay (mask tint + contour, without arrows)
|
| 835 |
-
mask255 = (mask01 * 255).astype(np.uint8)
|
| 836 |
-
mask3 = cv2.merge([mask255, mask255, mask255])
|
| 837 |
-
red = np.zeros_like(roi); red[:] = (0, 0, 255)
|
| 838 |
-
alpha = 0.55
|
| 839 |
-
tinted = cv2.addWeighted(roi, 1 - alpha, red, alpha, 0)
|
| 840 |
-
if mask255.any():
|
| 841 |
-
roi_overlay = np.where(mask3 > 0, tinted, roi)
|
| 842 |
-
cnts, _ = cv2.findContours(mask255, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
|
| 843 |
-
cv2.drawContours(roi_overlay, cnts, -1, (255, 255, 255), 2)
|
| 844 |
-
else:
|
| 845 |
-
roi_overlay = anno_roi
|
| 846 |
-
|
| 847 |
-
seg_full = image_cv.copy()
|
| 848 |
-
seg_full[y1:y2, x1:x2] = roi_overlay
|
| 849 |
-
segmentation_path = os.path.join(out_dir, f"segmentation_{ts}.png")
|
| 850 |
-
cv2.imwrite(segmentation_path, seg_full)
|
| 851 |
-
|
| 852 |
-
segmentation_roi_path = os.path.join(out_dir, f"segmentation_roi_{ts}.png")
|
| 853 |
-
cv2.imwrite(segmentation_roi_path, roi_overlay)
|
| 854 |
-
|
| 855 |
-
# Annotated (mask + arrows + labels) in full-frame
|
| 856 |
-
anno_full = image_cv.copy()
|
| 857 |
-
anno_full[y1:y2, x1:x2] = anno_roi
|
| 858 |
-
annotated_seg_path = os.path.join(out_dir, f"segmentation_annotated_{ts}.png")
|
| 859 |
-
cv2.imwrite(annotated_seg_path, anno_full)
|
| 860 |
-
|
| 861 |
-
# --- Optional classification ---
|
| 862 |
-
wound_type = "Unknown"
|
| 863 |
-
cls_pipe = self.models_cache.get("cls")
|
| 864 |
-
if cls_pipe is not None:
|
| 865 |
-
try:
|
| 866 |
-
preds = cls_pipe(Image.fromarray(cv2.cvtColor(roi, cv2.COLOR_BGR2RGB)))
|
| 867 |
-
if preds:
|
| 868 |
-
wound_type = max(preds, key=lambda x: x.get("score", 0)).get("label", "Unknown")
|
| 869 |
-
except Exception as e:
|
| 870 |
-
logging.warning(f"Classification failed: {e}")
|
| 871 |
-
|
| 872 |
-
# Log end-of-seg summary
|
| 873 |
-
seg_summary = {
|
| 874 |
-
"seg_used": seg_debug.get("used"),
|
| 875 |
-
"seg_reason": seg_debug.get("reason"),
|
| 876 |
-
"positive_fraction": round(float(seg_debug.get("positive_fraction", 0.0)), 6),
|
| 877 |
-
"threshold": seg_debug.get("thr"),
|
| 878 |
-
"segmentation_empty": segmentation_empty,
|
| 879 |
-
"exif_px_per_cm": round(px_per_cm, 3),
|
| 880 |
-
}
|
| 881 |
-
_log_kv("SEG_SUMMARY", seg_summary)
|
| 882 |
-
|
| 883 |
-
return {
|
| 884 |
-
"wound_type": wound_type,
|
| 885 |
-
"length_cm": length_cm,
|
| 886 |
-
"breadth_cm": breadth_cm,
|
| 887 |
-
"surface_area_cm2": surface_area_cm2,
|
| 888 |
-
"px_per_cm": round(px_per_cm, 2),
|
| 889 |
-
"calibration_meta": exif_meta,
|
| 890 |
-
"detection_confidence": float(results[0].boxes.conf[0].cpu().item())
|
| 891 |
-
if getattr(results[0].boxes, "conf", None) is not None else 0.0,
|
| 892 |
-
"detection_image_path": detection_path,
|
| 893 |
-
"segmentation_image_path": annotated_seg_path,
|
| 894 |
-
"segmentation_annotated_path": annotated_seg_path,
|
| 895 |
-
"segmentation_roi_path": segmentation_roi_path,
|
| 896 |
-
"roi_mask_path": roi_mask_path,
|
| 897 |
-
"segmentation_empty": segmentation_empty,
|
| 898 |
-
"segmentation_debug": seg_debug,
|
| 899 |
-
"original_image_path": original_path,
|
| 900 |
-
}
|
| 901 |
-
except Exception as e:
|
| 902 |
-
logging.error(f"Visual analysis failed: {e}", exc_info=True)
|
| 903 |
-
raise
|
| 904 |
-
|
| 905 |
-
# ---------- Knowledge base + reporting ----------
|
| 906 |
-
def query_guidelines(self, query: str) -> str:
|
| 907 |
-
try:
|
| 908 |
-
vs = self.knowledge_base_cache.get("vector_store")
|
| 909 |
-
if not vs:
|
| 910 |
-
return "Knowledge base is not available."
|
| 911 |
-
retriever = vs.as_retriever(search_kwargs={"k": 5})
|
| 912 |
-
docs = retriever.invoke(query)
|
| 913 |
-
lines: List[str] = []
|
| 914 |
-
for d in docs:
|
| 915 |
-
src = (d.metadata or {}).get("source", "N/A")
|
| 916 |
-
txt = (d.page_content or "")[:300]
|
| 917 |
-
lines.append(f"Source: {src}\nContent: {txt}...")
|
| 918 |
-
return "\n\n".join(lines) if lines else "No relevant guideline snippets found."
|
| 919 |
-
except Exception as e:
|
| 920 |
-
logging.warning(f"Guidelines query failed: {e}")
|
| 921 |
-
return f"Guidelines query failed: {str(e)}"
|
| 922 |
-
|
| 923 |
-
def _generate_fallback_report(self, patient_info: str, visual_results: Dict, guideline_context: str) -> str:
|
| 924 |
-
return f"""# 🩺 SmartHeal AI - Comprehensive Wound Analysis Report
|
| 925 |
-
## 📋 Patient Information
|
| 926 |
-
{patient_info}
|
| 927 |
-
## 🔍 Visual Analysis Results
|
| 928 |
-
- **Wound Type**: {visual_results.get('wound_type', 'Unknown')}
|
| 929 |
-
- **Dimensions**: {visual_results.get('length_cm', 0)} cm × {visual_results.get('breadth_cm', 0)} cm
|
| 930 |
-
- **Surface Area**: {visual_results.get('surface_area_cm2', 0)} cm²
|
| 931 |
-
- **Detection Confidence**: {visual_results.get('detection_confidence', 0):.1%}
|
| 932 |
-
- **Calibration**: {visual_results.get('px_per_cm','?')} px/cm ({(visual_results.get('calibration_meta') or {}).get('used','default')})
|
| 933 |
-
## 📊 Analysis Images
|
| 934 |
-
- **Original**: {visual_results.get('original_image_path', 'N/A')}
|
| 935 |
-
- **Detection**: {visual_results.get('detection_image_path', 'N/A')}
|
| 936 |
-
- **Segmentation**: {visual_results.get('segmentation_image_path', 'N/A')}
|
| 937 |
-
- **Annotated**: {visual_results.get('segmentation_annotated_path', 'N/A')}
|
| 938 |
-
## 🎯 Clinical Summary
|
| 939 |
-
Automated analysis provides quantitative measurements; verify via clinical examination.
|
| 940 |
-
## 💊 Recommendations
|
| 941 |
-
- Cleanse wound gently; select dressing per exudate/infection risk
|
| 942 |
-
- Debride necrotic tissue if indicated (clinical decision)
|
| 943 |
-
- Document with serial photos and measurements
|
| 944 |
-
## 📅 Monitoring
|
| 945 |
-
- Daily in week 1, then every 2–3 days (or as indicated)
|
| 946 |
-
- Weekly progress review
|
| 947 |
-
## 📚 Guideline Context
|
| 948 |
-
{(guideline_context or '')[:800]}{"..." if guideline_context and len(guideline_context) > 800 else ''}
|
| 949 |
-
**Disclaimer:** Automated, for decision support only. Verify clinically.
|
| 950 |
-
"""
|
| 951 |
-
|
| 952 |
-
def generate_final_report(
|
| 953 |
-
self,
|
| 954 |
-
patient_info: str,
|
| 955 |
-
visual_results: Dict,
|
| 956 |
-
guideline_context: str,
|
| 957 |
-
image_pil: Image.Image,
|
| 958 |
-
max_new_tokens: Optional[int] = None,
|
| 959 |
-
) -> str:
|
| 960 |
-
try:
|
| 961 |
-
report = generate_medgemma_report(
|
| 962 |
-
patient_info, visual_results, guideline_context, image_pil, max_new_tokens
|
| 963 |
)
|
| 964 |
-
|
| 965 |
-
return report
|
| 966 |
-
logging.warning("VLM unavailable/invalid; using fallback.")
|
| 967 |
-
return self._generate_fallback_report(patient_info, visual_results, guideline_context)
|
| 968 |
except Exception as e:
|
| 969 |
-
logging.error(f"
|
| 970 |
-
|
| 971 |
-
|
| 972 |
-
def save_and_commit_image(self, image_pil: Image.Image) -> str:
|
| 973 |
-
try:
|
| 974 |
-
os.makedirs(self.uploads_dir, exist_ok=True)
|
| 975 |
-
ts = datetime.now().strftime("%Y%m%d_%H%M%S")
|
| 976 |
-
filename = f"{ts}.png"
|
| 977 |
-
path = os.path.join(self.uploads_dir, filename)
|
| 978 |
-
image_pil.convert("RGB").save(path)
|
| 979 |
-
logging.info(f"✅ Image saved locally: {path}")
|
| 980 |
-
|
| 981 |
-
if HF_TOKEN and DATASET_ID:
|
| 982 |
-
try:
|
| 983 |
-
HfApi, HfFolder = _import_hf_hub()
|
| 984 |
-
HfFolder.save_token(HF_TOKEN)
|
| 985 |
-
api = HfApi()
|
| 986 |
-
api.upload_file(
|
| 987 |
-
path_or_fileobj=path,
|
| 988 |
-
path_in_repo=f"images/{filename}",
|
| 989 |
-
repo_id=DATASET_ID,
|
| 990 |
-
repo_type="dataset",
|
| 991 |
-
token=HF_TOKEN,
|
| 992 |
-
commit_message=f"Upload wound image: {filename}",
|
| 993 |
-
)
|
| 994 |
-
logging.info("✅ Image committed to HF dataset")
|
| 995 |
-
except Exception as e:
|
| 996 |
-
logging.warning(f"HF upload failed: {e}")
|
| 997 |
-
|
| 998 |
-
return path
|
| 999 |
-
except Exception as e:
|
| 1000 |
-
logging.error(f"Failed to save/commit image: {e}")
|
| 1001 |
-
return ""
|
| 1002 |
-
|
| 1003 |
-
def full_analysis_pipeline(self, image_pil: Image.Image, questionnaire_data: Dict) -> Dict:
|
| 1004 |
-
try:
|
| 1005 |
-
saved_path = self.save_and_commit_image(image_pil)
|
| 1006 |
-
visual_results = self.perform_visual_analysis(image_pil)
|
| 1007 |
-
|
| 1008 |
-
pi = questionnaire_data or {}
|
| 1009 |
-
patient_info = (
|
| 1010 |
-
f"Age: {pi.get('age','N/A')}, "
|
| 1011 |
-
f"Diabetic: {pi.get('diabetic','N/A')}, "
|
| 1012 |
-
f"Allergies: {pi.get('allergies','N/A')}, "
|
| 1013 |
-
f"Date of Wound: {pi.get('date_of_injury','N/A')}, "
|
| 1014 |
-
f"Professional Care: {pi.get('professional_care','N/A')}, "
|
| 1015 |
-
f"Oozing/Bleeding: {pi.get('oozing_bleeding','N/A')}, "
|
| 1016 |
-
f"Infection: {pi.get('infection','N/A')}, "
|
| 1017 |
-
f"Moisture: {pi.get('moisture','N/A')}"
|
| 1018 |
-
)
|
| 1019 |
-
|
| 1020 |
-
query = (
|
| 1021 |
-
f"best practices for managing a {visual_results.get('wound_type','Unknown')} "
|
| 1022 |
-
f"with moisture '{pi.get('moisture','unknown')}' and infection '{pi.get('infection','unknown')}' "
|
| 1023 |
-
f"in a diabetic status '{pi.get('diabetic','unknown')}'"
|
| 1024 |
-
)
|
| 1025 |
-
guideline_context = self.query_guidelines(query)
|
| 1026 |
|
| 1027 |
-
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1028 |
|
| 1029 |
-
return {
|
| 1030 |
-
"success": True,
|
| 1031 |
-
"visual_analysis": visual_results,
|
| 1032 |
-
"report": report,
|
| 1033 |
-
"saved_image_path": saved_path,
|
| 1034 |
-
"guideline_context": (guideline_context or "")[:500] + (
|
| 1035 |
-
"..." if guideline_context and len(guideline_context) > 500 else ""
|
| 1036 |
-
),
|
| 1037 |
-
}
|
| 1038 |
-
except Exception as e:
|
| 1039 |
-
logging.error(f"Pipeline error: {e}")
|
| 1040 |
-
return {
|
| 1041 |
-
"success": False,
|
| 1042 |
-
"error": str(e),
|
| 1043 |
-
"visual_analysis": {},
|
| 1044 |
-
"report": f"Analysis failed: {str(e)}",
|
| 1045 |
-
"saved_image_path": None,
|
| 1046 |
-
"guideline_context": "",
|
| 1047 |
-
}
|
| 1048 |
|
| 1049 |
-
|
| 1050 |
-
|
| 1051 |
-
|
| 1052 |
-
|
| 1053 |
-
|
| 1054 |
-
|
| 1055 |
-
|
| 1056 |
-
|
| 1057 |
-
|
| 1058 |
-
image_pil = Image.fromarray(image)
|
| 1059 |
-
else:
|
| 1060 |
-
raise ValueError(f"Unsupported image type: {type(image)}")
|
| 1061 |
|
| 1062 |
-
|
| 1063 |
-
|
| 1064 |
-
logging.error(f"Wound analysis error: {e}")
|
| 1065 |
-
return {
|
| 1066 |
-
"success": False,
|
| 1067 |
-
"error": str(e),
|
| 1068 |
-
"visual_analysis": {},
|
| 1069 |
-
"report": f"Analysis initialization failed: {str(e)}",
|
| 1070 |
-
"saved_image_path": None,
|
| 1071 |
-
"guideline_context": "",
|
| 1072 |
-
}
|
|
|
|
| 1 |
+
#!/usr/bin/env python3
|
|
|
|
|
|
|
| 2 |
|
| 3 |
import os
|
| 4 |
import logging
|
| 5 |
+
import traceback
|
| 6 |
+
import gradio as gr
|
| 7 |
+
import spaces
|
| 8 |
|
| 9 |
+
# Import internal modules
|
| 10 |
+
from src.config import Config
|
| 11 |
+
from src.database import DatabaseManager
|
| 12 |
+
from src.auth import AuthManager
|
| 13 |
+
from src.ai_processor import AIProcessor
|
| 14 |
+
from src.ui_components_original import UIComponents
|
| 15 |
|
| 16 |
+
# Logging setup
|
| 17 |
+
logging.basicConfig(level=logging.INFO, format='%(asctime)s - %(levelname)s - %(message)s')
|
|
|
|
|
|
|
| 18 |
|
| 19 |
+
class SmartHealApp:
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| 20 |
def __init__(self):
|
| 21 |
+
self.ui_components = None
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| 22 |
+
try:
|
| 23 |
+
self.config = Config()
|
| 24 |
+
self.database_manager = DatabaseManager(self.config.get_mysql_config())
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| 25 |
+
self.auth_manager = AuthManager(self.database_manager)
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| 26 |
+
self.ai_processor = AIProcessor()
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| 27 |
+
self.ui_components = UIComponents(
|
| 28 |
+
self.auth_manager,
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| 29 |
+
self.database_manager,
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| 30 |
+
self.ai_processor
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| 31 |
)
|
| 32 |
+
logging.info("✅ SmartHeal App initialized successfully.")
|
|
|
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|
| 33 |
except Exception as e:
|
| 34 |
+
logging.error(f"Initialization error: {e}")
|
| 35 |
+
traceback.print_exc()
|
| 36 |
+
raise
|
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|
| 37 |
|
| 38 |
+
def launch(self, port=7860, share=True):
|
| 39 |
+
interface = self.ui_components.create_interface()
|
| 40 |
+
interface.launch(
|
| 41 |
+
share=share
|
| 42 |
+
)
|
| 43 |
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|
| 44 |
|
| 45 |
+
def main():
|
| 46 |
+
try:
|
| 47 |
+
app = SmartHealApp()
|
| 48 |
+
app.launch()
|
| 49 |
+
except KeyboardInterrupt:
|
| 50 |
+
logging.info("App interrupted by user.")
|
| 51 |
+
except Exception:
|
| 52 |
+
logging.error("App failed to start.")
|
| 53 |
+
raise
|
|
|
|
|
|
|
|
|
|
| 54 |
|
| 55 |
+
if __name__ == "__main__":
|
| 56 |
+
main()
|
|
|
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