app.py

import gradio as gr
import tempfile, os, shutil, zipfile, glob, time
import os
from PIL import Image, ImageDraw, ImageFont
os.environ["GRADIO_TEMP_DIR"] = "/tmp/gradio"
os.environ["TMPDIR"] = "/tmp"
os.environ["HF_HOME"] = "/tmp/hfhome"
os.environ["HF_HUB_CACHE"] = "/tmp/hfhome/hub"
os.environ["XDG_CACHE_HOME"] = "/tmp/xdgcache"   # au cas où
os.environ["TORCH_HOME"] = "/tmp/torchhome"
import numpy as np
import pandas as pd
import torch
from torchvision import transforms
from transformers import SegformerForSemanticSegmentation
import tifffile
from scipy.ndimage import label
from huggingface_hub import hf_hub_download
PREVSIZE=600
PLACEHOLDER_W, PLACEHOLDER_H = PREVSIZE, 340
PLACEHOLDER = Image.new("RGB", (PLACEHOLDER_W, PLACEHOLDER_H), (245, 245, 245))

def _safe_rmtree(p):
    try: shutil.rmtree(p, ignore_errors=True)
    except Exception: pass

# -- ménage de démarrage (si quelque chose traîne) --
for _p in ["/home/user/.cache", "/home/user/.local/share/Trash", "/home/user/app/tmp"]:
    _safe_rmtree(_p)
CACHE_DIR = "/tmp/hfhome/transformers"  # même valeur que ci-dessus

for _p in ["/home/user/.cache", "/home/user/.local/share/Trash", "/home/user/app/tmp","/home/user/.gradio", "/tmp/gradio", "/tmp/hfhome", "/tmp/xdgcache", "/tmp/torchhome"]:
    _safe_rmtree(_p)

# ======== CONFIG ========
DEVICE = "cpu"                       # Space CPU
TARGET_SIZE = (341, 512)
AR_MODEL_ID = "RomainFernandez/MicroDeepAerenchyma-Lacuna"
CE_MODEL_ID = "RomainFernandez/MicroDeepAerenchyma-Cortex"

# (Optionnel) dataset de démo -> stocke un petit ZIP (qq images 341x512 ou proches)
DEMO_DATASET_ID = "RomainFernandez/MicroDeepAerenchyma-Demo"  # à créer par toi
DEMO_ZIP_FILENAME = "demo_images.zip"  # mets ce nom dans le dataset

# ======== MODELS (load once) ========
ar_model = SegformerForSemanticSegmentation.from_pretrained(
    AR_MODEL_ID, cache_dir=CACHE_DIR).to(DEVICE).eval()
ce_model = SegformerForSemanticSegmentation.from_pretrained(
    CE_MODEL_ID, cache_dir=CACHE_DIR).to(DEVICE).eval()


# ---- PURGE OPTIONNELLE DU CACHE HF (réduit l'usage disque) ----
try:
    from huggingface_hub import scan_cache_dir
    # CACHE_DIR = "/tmp/hfhome/transformers"  -> on monte d'un cran: "/tmp/hfhome"
    cache_root = os.path.abspath(os.path.join(CACHE_DIR, ".."))
    info = scan_cache_dir(cache_root)

    # ne garder que les 2 dépôts utiles à l'app
    keep = {AR_MODEL_ID, CE_MODEL_ID}
    for repo in info.repos:
        if getattr(repo, "repo_id", None) not in keep:
            # supprime entièrement le repo non utilisé
            repo_path = getattr(repo, "repo_path", None)
            if repo_path and os.path.exists(repo_path):
                _safe_rmtree(repo_path)
except Exception:
    # pas bloquant si la structure du cache change
    pass



transform = transforms.Compose([
    transforms.Resize(TARGET_SIZE),
    transforms.ToTensor(),
    transforms.Lambda(lambda x: x.repeat(3, 1, 1))  # grayscale -> 3 canaux (SegFormer)
])

def predict_mask(model, image_L):
    x = transform(image_L).unsqueeze(0).to(DEVICE)
    with torch.no_grad():
        logits = model(x).logits
        up = torch.nn.functional.interpolate(logits, size=x.shape[-2:], mode="bilinear", align_corners=False)
        pred = torch.argmax(up, dim=1)[0].cpu().numpy()
    return pred

def largest_cc(binary):
    lab, n = label(binary)
    if n == 0: return binary*0
    largest = np.argmax(np.bincount(lab.flat)[1:]) + 1
    return (lab == largest).astype(np.uint8)

def safe_list_images(root):
    exts = (".png",".jpg",".jpeg",".tif",".tiff")
    out = []
    for p in glob.glob(os.path.join(root, "**/*"), recursive=True):
        if os.path.isfile(p) and p.lower().endswith(exts):
            out.append(p)
    return sorted(out)

# On garde trace des répertoires temporaires de la session
ACTIVE_WORKDIRS = set()
BUSY = False

def overlay_counter(img_np: np.ndarray, idx: int, total: int) -> Image.Image:
    """Ajoute 'Image idx/total' en haut-gauche, fond noir, police plus grande."""
    im = Image.fromarray(img_np) if isinstance(img_np, np.ndarray) else img_np.copy()
    draw = ImageDraw.Draw(im)

    text = f"Image {idx}/{total}"

    # Taille de police proportionnelle à la largeur de l'image (≈ 3%)
    # min/max pour éviter trop petit/grand
    try:
        W = im.width
    except Exception:
        W = 800
    fontsize = max(18, min(int(W * 0.03), 48))

    # Essaie une vraie police (HF Spaces a en général DejaVuSans)
    try:
        font = ImageFont.truetype("/usr/share/fonts/truetype/dejavu/DejaVuSans-Bold.ttf", fontsize)
    except Exception:
        try:
            font = ImageFont.truetype("/usr/share/fonts/truetype/dejavu/DejaVuSans.ttf", fontsize)
        except Exception:
            font = ImageFont.load_default()  # fallback

    pad_x, pad_y = max(6, fontsize // 3), max(4, fontsize // 4)
    # bbox du texte
    left, top, right, bottom = draw.textbbox((0, 0), text, font=font)
    tw, th = right - left, bottom - top
    box = (0, 0, tw + 2 * pad_x, th + 2 * pad_y)

    # fond noir (opaque). Si tu veux semi-opaque, convertis en RGBA + composite.
    draw.rectangle(box, fill=(0, 0, 0))
    draw.text((pad_x, pad_y), text, fill=(255, 255, 255), font=font)

    return im

def run_job(files_or_zip, use_demo=False, progress=gr.Progress()):
    # garde: espace disque minimal requis (ex: 5 Go)
    MIN_FREE = 5 * (1024**3)
    try:
        usage = shutil.disk_usage("/")
        if usage.free < MIN_FREE:
            yield None, (
                "⚠️ Low free disk on Space. Please retry later "
                "(administrator: increase persistent storage or clean caches)."
            ), current_preview, None
            return
    except Exception:
        pass
   
    global BUSY
    first_img_time = None  # durée mesurée sur la 1ère image
    current_preview = PLACEHOLDER.copy()


    # Refuser immédiatement si un autre job tourne
    if BUSY:
        yield None, (
            "⚠️ Server already in use — please come back in a few minutes "
            "(another batch is running on this CPU Space)."
        ), current_preview, None
        return

#    BUSY = True

    try:
        previews = []  # liste d’images PIL pour la galerie
        # --- Prépare un espace de travail éphémère ---
        workdir = tempfile.mkdtemp(prefix="job_")
        ACTIVE_WORKDIRS.add(workdir)
        in_root  = os.path.join(workdir, "in")
        out_root = os.path.join(workdir, "out")
        os.makedirs(in_root, exist_ok=True)
        os.makedirs(out_root, exist_ok=True)

    # --- Récupère les entrées ---
        file_list = []
        if use_demo:
            demo_zip = hf_hub_download(repo_id=DEMO_DATASET_ID, filename=DEMO_ZIP_FILENAME, repo_type="dataset")
            with zipfile.ZipFile(demo_zip) as z:
                z.extractall(in_root)
            file_list = safe_list_images(in_root)
            total = len(file_list)
            previews = []  # images pour la galerie

        else:
            # files_or_zip est une LISTE de chemins (strings) quand type="filepath"
            paths = files_or_zip or []
            for p in paths:
                if not p:
                    continue
                src = p if isinstance(p, str) else p.name
                if src.lower().endswith(".zip"):
                    with zipfile.ZipFile(src) as z:
                        z.extractall(in_root)
                else:
                    # copie d'un fichier image individuel
                    shutil.copy(src, os.path.join(in_root, os.path.basename(src)))
            file_list = safe_list_images(in_root)
            total = len(file_list)
            previews = []  # images pour la galerie

        if not file_list:
            yield None, "No images found. Upload multiple images or a ZIP (recommended for folders).", current_preview, None
            return
        start = time.time()
        # --- constants for RAW contrast ---
        p_lo, p_hi, gamma = 5.0, 99.5, 1.30

        yield None, f"Found {total} image(s). Starting…", current_preview, workdir
        progress(0.0)  # initialise

        # Regroupe par sous-dossier relatif (pour mirrorer la sortie)
        rel_map = {}
        for p in file_list:
            rel = os.path.relpath(p, in_root)
            rel_dir = os.path.dirname(rel)  # "" si racine
            rel_map.setdefault(rel_dir, []).append(p)

        processed = 0
        for rel_dir, paths in rel_map.items():
            out_dir   = os.path.join(out_root, rel_dir)
            pred_dir  = os.path.join(out_dir, "predicted_images")
            ar_dir    = os.path.join(pred_dir, "pred_AR")
            cortex_dir= os.path.join(pred_dir, "pred_Cortex")
            endo_dir  = os.path.join(pred_dir, "pred_Endoderm")
            global_dir= os.path.join(pred_dir, "pred_global")
            for d in [ar_dir, cortex_dir, endo_dir, global_dir]:
                os.makedirs(d, exist_ok=True)

            rows = []
            for p in paths:
                image_name = os.path.basename(p)
                #yield None, f"Processing {image_name}…", previews,workdir
                progress(processed / total if total > 0 else 0.0)

                im = Image.open(p).convert("L")
                # ---- PREVIEW RAW à T/4 (à partir de la 2e image) ----
                # On fabrique un RAW "hint" à la taille du réseau (TARGET_SIZE: H=341, W=512)
                w_hint, h_hint = TARGET_SIZE[1], TARGET_SIZE[0]
                imr_hint = im.resize((w_hint, h_hint), Image.BILINEAR)
                raw_hint = np.array(imr_hint, dtype=np.uint8)

                # contraste doux
                lo_hint, hi_hint = np.percentile(raw_hint, (p_lo, p_hi))
                if hi_hint > lo_hint:
                    x = (raw_hint.astype(np.float32) - lo_hint) / (hi_hint - lo_hint)
                    x = np.clip(x, 0.0, 1.0)
                    x = np.power(x, 1.0 / gamma)
                    raw_boost_hint = (x * 255.0).astype(np.uint8)
                else:
                    raw_boost_hint = raw_hint

                raw_rgb_hint = np.repeat(raw_boost_hint[..., None], 3, axis=-1).astype(np.uint8)
                black = np.zeros_like(raw_rgb_hint, dtype=np.uint8)
                interim = np.concatenate([raw_rgb_hint, black], axis=1).astype(np.uint8)

                # à partir de la 2e image, attendre T/4 (max 0.30s), puis publier l'intermédiaire
                if (processed >= 1) and (first_img_time is not None) and (first_img_time > 0):
                    delay = min(0.7 * first_img_time, 2)
                    if delay > 0.02:
                        time.sleep(delay)
                    interim_prev = overlay_counter(interim, processed + 1, total)
                    if interim_prev.width > PREVSIZE:
                        hh = int(interim_prev.height * (PREVSIZE / interim_prev.width))
                        interim_prev = interim_prev.resize((PREVSIZE, hh), Image.LANCZOS)
                    current_preview = interim_prev
                    yield None, f"Preview (RAW) {processed+1}/{total}: {image_name}", current_preview, workdir



                # Prédictions
                t0 = time.time() if processed == 0 else None
                pred_ar = predict_mask(ar_model, im)
                pred_ce = predict_mask(ce_model, im)

                mask_ar     = (pred_ar == 1).astype(np.uint8)*255
                mask_cortex = (pred_ce == 1).astype(np.uint8)*255
                mask_endo   = (pred_ce == 2).astype(np.uint8)*255

                # Plus grande composante CE
                combined_ce = ((mask_cortex > 0) | (mask_endo > 0)).astype(np.uint8)
                largest     = largest_cc(combined_ce)

                ar_in     = ((mask_ar > 0) & (largest > 0)).astype(np.uint8)
                cortex_in = ((mask_cortex > 0) & (largest > 0)).astype(np.uint8)

                total_ce      = int(largest.sum())
                total_cortex  = int(cortex_in.sum())
                ar_px         = int(ar_in.sum())
                AR_in_CE      = (ar_px / total_ce * 100) if total_ce > 0 else 0.0
                AR_in_Cortex  = (ar_px / total_cortex * 100) if total_cortex > 0 else 0.0

                rows.append({
                    "image_name": image_name,
                    "AR_percent_in_Cortex+Endoderm": AR_in_CE,
                    "AR_percent_in_Cortex_only": AR_in_Cortex,
                    "Cortex_surface_in_pixels": total_cortex,
                    "Stele_surface_in_pixels":total_ce-total_cortex,
                    "AR_surface_in_pixels": ar_px
                })

                for d in (ar_dir, cortex_dir, endo_dir, global_dir):
                    os.makedirs(d, exist_ok=True)

                # Écrit avec garde-fous
                try:
                    tifffile.imwrite(os.path.join(ar_dir, image_name), mask_ar,    compression="deflate")
                except FileNotFoundError:
                    os.makedirs(ar_dir, exist_ok=True)
                    tifffile.imwrite(os.path.join(ar_dir, image_name), mask_ar,    compression="deflate")

                try:
                    tifffile.imwrite(os.path.join(cortex_dir, image_name), mask_cortex,    compression="deflate")
                except FileNotFoundError:
                    os.makedirs(cortex_dir, exist_ok=True)
                    tifffile.imwrite(os.path.join(cortex_dir, image_name), mask_cortex,    compression="deflate")

                try:
                    tifffile.imwrite(os.path.join(endo_dir, image_name), mask_endo,    compression="deflate")
                except FileNotFoundError:
                    os.makedirs(endo_dir, exist_ok=True)
                    tifffile.imwrite(os.path.join(endo_dir, image_name), mask_endo,    compression="deflate")

                # Panel TIFF [raw_boost | overlay RGB]
                h, w = mask_ar.shape
                imr  = im.resize((w, h), Image.BILINEAR)
                raw  = np.array(imr, dtype=np.uint8)

                # --- RAW contrast (softer) ---
                # percentiles un peu plus serrés pour réduire l'écrêtage
                p_lo, p_hi = 5.0, 99.5
                lo, hi = np.percentile(raw, (p_lo, p_hi))

                if hi > lo:
                    # mise à l'échelle linéaire 0..1
                    x = (raw.astype(np.float32) - lo) / (hi - lo)
                    x = np.clip(x, 0.0, 1.0)
                    # courbe gamma douce (>1 comprime les hautes lumières)
                    gamma = 1.30
                    x = np.power(x, 1.0 / gamma)   # 1/gamma ~ 0.833
                    raw_boost = (x * 255.0).astype(np.uint8)
                else:
                    raw_boost = raw

                raw_rgb = np.repeat(raw_boost[..., None], 3, axis=-1).astype(np.uint8)
                RED_SCALE, GREEN_SCALE = 0.5, 0.3  # ajustables

                r = np.clip(mask_ar.astype(np.float32) * RED_SCALE, 0, 255).astype(np.uint8)
                g = np.clip(mask_cortex.astype(np.float32) * GREEN_SCALE, 0, 255).astype(np.uint8)
                b = raw_boost  # on garde le raw inchangé en B (tu peux mettre raw_boost si tu préfères)

                rgb = np.stack([r, g, b], axis=-1)





                panel   = np.concatenate([raw_rgb, rgb], axis=1).astype(np.uint8)

                base = os.path.splitext(image_name)[0]
                os.makedirs(global_dir, exist_ok=True)
                tifffile.imwrite(os.path.join(global_dir, base + "_panel.tif"), panel, photometric="rgb",    compression="deflate")
                # Aperçu avec compteur (idx=processed+1)
                
                # fixe la durée de référence après la 1re image
                if t0 is not None and first_img_time is None:
                    first_img_time = max(0.02, time.time() - t0)  # borne basse 20 ms

                preview_img = overlay_counter(panel, processed + 1, total)
                # miniature raisonnable (éviter des images immenses côté client)
                maxw = PREVSIZE
                if preview_img.width > maxw:
                    h = int(preview_img.height * (maxw / preview_img.width))
                    preview_img = preview_img.resize((maxw, h), Image.LANCZOS)
                current_preview = preview_img  # <- on remplace l’aperçu courant

                yield None, f"Processed {processed+1}/{total}: {image_name}", current_preview, workdir
                processed += 1
                progress(processed / total if total > 0 else 1.0)
                #yield None, f"Processed {processed}/{len(file_list)}: {image_name}", current_preview, workdir

            if rows:
                os.makedirs(out_dir, exist_ok=True)
                pd.DataFrame(rows).to_csv(os.path.join(out_dir, "pred_metrics.csv"), index=False)

        # ZIP final
        zip_path = os.path.join(workdir, "results.zip")
        shutil.make_archive(zip_path[:-4], "zip", out_root)
        
        #  libère l’espace immédiatement : on supprime le dossier des sorties
        _safe_rmtree(out_root)
        
        elapsed = time.time() - start
        yield zip_path, f"Done. {processed} image(s) in {elapsed:.1f}s. Download the ZIP below.", current_preview, workdir
        # On ne supprime pas ici pour laisser le téléchargement se faire
    finally:
        BUSY = False


def cleanup_all():
    # Appelé à la fin de la session utilisateur
    for wd in list(ACTIVE_WORKDIRS):
        try:
            _safe_rmtree(wd)
            shutil.rmtree(wd, ignore_errors=True)
            ACTIVE_WORKDIRS.discard(wd)
        except Exception:
            pass
    # purge des caches au cas où
    for _p in ["/tmp/hfhome", "/tmp/xdgcache", "/tmp/torchhome"]:
        _safe_rmtree(_p)
        
    for wd in list(ACTIVE_WORKDIRS):
        try:
            _safe_rmtree(wd)
            ACTIVE_WORKDIRS.discard(wd)
        except Exception:
            pass
    # Purge de tous les caches/temp usuels
    for _p in [
        "/tmp/gradio", "/tmp/hfhome", "/tmp/xdgcache", "/tmp/torchhome",
        "/home/user/.cache", "/home/user/.gradio", "/home/user/.local/share/Trash"
    ]:
        _safe_rmtree(_p)

with gr.Blocks(theme=gr.themes.Soft(), title="MicroDeepAerenchyma — Segmentation (CPU)") as demo:
    BANNER_URL = "https://huggingface.co/spaces/RomainFernandez/DeepAerenchyma/resolve/main/banner.png"

    gr.HTML(f"""
    <style>
    .banner-wrap {{ margin: 4px 0 6px; text-align:center; }}  /* marge réduite */
    .banner-wrap img {{
        display:inline-block;
        max-width:100%;
        height:auto;
        max-height:clamp(140px, 24vh, 256px);
        border-radius:12px;
        box-shadow: 0 2px 8px rgba(0,0,0,.08);
    }}
    /* ces règles peuvent rester si tu veux affiner plus tard
    .prose h1:first-child {{ margin-top: 0.1rem !important; margin-bottom: 0.1rem !important; }}
    .prose p {{ margin-top: 0.1rem !important; margin-bottom: 0.1rem !important; }}
    */
    </style>
    <div class="banner-wrap">
    <img src="{BANNER_URL}" alt="Deep Aerenchyma">
    </div>
    """)
    gr.HTML("""
    <style>
    #live_preview { min-height: 220px; }   /* réserve une hauteur, évite les sauts */
    #live_preview img { width: 100% !important; height: auto !important; object-fit: contain; }
    </style>
    """)
    gr.HTML("""
    <style>
    /* réduire la largeur visuelle et la typo du Files */
    #uploader * { font-size: 0.92rem !important; }
    /* zone de drop compacte (selector robuste via testid présent en v5) */
    #uploader [data-testid="dropzone"] {
        min-height: 84px !important;
        padding: 8px !important;
    }
    </style>
    """)
    gr.HTML("""
    <style>
    html, body { height: 100%; overflow-y: auto !important; }
    .gradio-container { min-height: 100vh; overflow-y: auto !important; }
    @media (max-width: 600px) {
        .gradio-container { padding: 8px !important; }
    }
    </style>
    """)
    gr.HTML("""
    <style>
    /* H1 un peu plus grand + compact */
    #titleblock h1 {
        font-size: 1.55rem !important;   /* ≈ +10–15% */
        line-height: 1.25 !important;
        margin: 6px 0 8px !important;     /* réduit l’espace sous le H1 */
    }
    #titleblock p {
        margin: 2px 0 6px !important;     /* compresse un peu les paragraphes */
    }
    </style>
    """)
    title_md = gr.Markdown(
    """
    # Deep Aerenchyma
    **High-throughput anatomical phenotyping based on Segformer**
    **Authors:** Hani Atef, Romain Fernandez (CIRAD, UMR AGAP, France)  
    **Funder:** Global Methane Hub, CIRAD Arize project

    Upload **multiple images** *or* **one ZIP** (supports nested folders).  
    Output: masks, result panels in `pred_global`, and `pred_metrics.csv`.
    """,
    elem_id="titleblock"
    )
        # Upload (ligne 1)
    with gr.Row():
        files = gr.Files(
            label="Upload images or one ZIP (recommended)",
            file_count="multiple",
            type="filepath",
            elem_id="uploader"   # <-- on va le styler
        )

    # Boutons (ligne 2)
    with gr.Row():
        start_btn = gr.Button("Start with my own images", variant="primary")
    with gr.Row():
        demo_btn  = gr.Button("Test with demo images", variant="primary")

    # Logs (ligne 5)
    with gr.Row():
        log = gr.Textbox(label="Logs", lines=4)

    # Préview (ligne 3)
    with gr.Row():
        live_preview = gr.Image(
            label="Live preview",
            value=PLACEHOLDER,
            interactive=False,
            elem_id="live_preview",
            height=None
        )


    # Download (ligne 4)
    with gr.Row():
        out_zip = gr.File(label="Download results (ZIP)")


    workdir_state = gr.State(value=None)
    def driver(files):
        from builtins import globals as _g
        if _g().get("BUSY", False):
            # toast + log immédiats (sans lancer le job)
            yield {log: "⚠️ Server already in use — please retry in a few minutes.",
                live_preview: PLACEHOLDER,
                workdir_state: None}
            return
        for zip_path, msg, preview, wd in run_job(files, use_demo=False):
            update = {log: msg, live_preview: preview, workdir_state: wd}
            if zip_path is not None:
                update[out_zip] = zip_path
            yield update

    def driver_demo():
        from builtins import globals as _g
        if _g().get("BUSY", False):
            yield {log: "⚠️ Server already in use — please retry in a few minutes.",
                live_preview: PLACEHOLDER,
                workdir_state: None}
            return
        for zip_path, msg, preview, wd in run_job(None, use_demo=True):
            update = {log: msg, live_preview: preview, workdir_state: wd}
            if zip_path is not None:
                update[out_zip] = zip_path
            yield update

    start_btn.click(
        driver,
        inputs=[files],
        outputs=[out_zip, log, live_preview, workdir_state],
        show_progress="hidden"      # <-- AJOUT
    )
    demo_btn.click(
        driver_demo,
        inputs=None,
        outputs=[out_zip, log, live_preview, workdir_state],
        show_progress="hidden"      # <-- AJOUT
    )
    demo.unload(lambda: cleanup_all())

demo.queue().launch(ssr_mode=False)