physics_based_augmentation/app.py

import time
import os
import io
import zipfile
from pathlib import Path
from typing import List, Tuple
from PIL import Image
import streamlit as st
import base64



def nav_to(p: str):
    st.session_state.page = p

# ---------- Theme-aware logo (top-right, base64-embedded) ----------
def _b64_img(path: str) -> str | None:
    try:
        with open(path, "rb") as f:
            return base64.b64encode(f.read()).decode("ascii")
    except Exception:
        return None

def header_with_theme_logo(title: str,
                           light_path: str = "logos/NEW_PHYSTECH_for_light.png",
                           dark_path: str = "logos/NEW_PHYSTECH_for_dark.png",
                           size_px: int = 100):
    light_b64 = _b64_img(light_path)
    dark_b64  = _b64_img(dark_path)
    if not (light_b64 or dark_b64):
        # если нет логотипов — просто выводим заголовок
        st.markdown(f"## {title}")
        return

    light_src = f"data:image/png;base64,{light_b64}" if light_b64 else ""
    dark_src = f"data:image/png;base64,{dark_b64}" if dark_b64 else light_src

    html = f"""
     <style>
       /* убираем стандартный padding контейнера Streamlit сверху */
       section.main > div:first-child {{
         padding-top: 0rem;
       }}
       .hdr {{
         display: flex; align-items: center; justify-content: space-between;
       }}
       .hdr h1 {{
         margin: 0;
         font-size: 3.5rem;
         line-height: 1.2;
       }}
       .hdr .logo img {{
         width: 250px; height: {size_px}px; object-fit: contain;
         border-radius: 8px;
         display: inline-block;
       }}
       .hdr .logo img.light {{ display: inline-block; }}
       .hdr .logo img.dark  {{ display: none; }}
       @media (prefers-color-scheme: dark) {{
         .hdr .logo img.light {{ display: none; }}
         .hdr .logo img.dark  {{ display: inline-block; }}
       }}
     </style>
     <div class="hdr">
       <h1>{title}</h1>
       <div class="logo">
         <img src="{light_src}" alt="logo" class="light" />
         <img src="{dark_src}"  alt="logo" class="dark" />
       </div>
     </div>
     """
    st.markdown(html, unsafe_allow_html=True)


st.set_page_config(
    page_title="MRI physics based augmentation",
    page_icon="🧠",
    layout="wide"
)
header_with_theme_logo("MRI physics based augmentation")

# ---------- Simple router in session_state ----------
if "page" not in st.session_state:
    st.session_state.page = "home"

# storage for generated phantom (appears after progress completes)
if "phantom_blob" not in st.session_state:
    st.session_state.phantom_blob = None
if "phantom_name" not in st.session_state:
    st.session_state.phantom_name = None



# ---------- Image helpers ----------
SUPPORTED_EXTS = (".png", ".jpg", ".jpeg", ".bmp", ".tif", ".tiff")
SUPPORTED_EXTS_PHANTOM = (".dcm", ".nii", ".nii.gz", ".nrrd", ".npy", ".png", ".jpg", ".jpeg")
MAX_VALUE_DATASET = 100000

def center_crop_to_square(img: Image.Image) -> Image.Image:
    """Center-crop PIL image to a square based on the smaller side."""
    w, h = img.size
    s = min(w, h)
    left = (w - s) // 2
    top = (h - s) // 2
    return img.crop((left, top, left + s, top + s))

def load_and_prepare_assets(asset_dir: str = "assets", count: int = 3, size: Tuple[int, int] = (320, 320)) -> List[Tuple[Image.Image, str]]:
    """Load up to `count` images from asset_dir, center-crop to square, resize to `size`."""
    results = []
    if not os.path.isdir(asset_dir):
        return results
    files = sorted([f for f in os.listdir(asset_dir) if os.path.splitext(f.lower())[1] in SUPPORTED_EXTS])
    for fname in files[:count]:
        path = os.path.join(asset_dir, fname)
        try:
            img = Image.open(path).convert("RGB")
            img = center_crop_to_square(img)
            img = img.resize(size, Image.LANCZOS)
            results.append((img, fname))
        except Exception:
            continue
    return results


def run_job_stub(status_placeholder, progress_placeholder, steps=None, delay=0.9):
    """Simulate a long-running job with progress and 3-line status stream.
       Returns True when finished."""
    if steps is None:
        steps = [
            "Инициализация пайплайна...",
            "Обработка входных данных...",
            "Генерация синтетических изображений...",
            "Постобработка результатов...",
            "Готово!",
        ]
    progress = 0
    last3 = []
    progress_placeholder.progress(progress, text="Waiting to start...")
    status_placeholder.markdown("")

    for i, msg in enumerate(steps, 1):
        last3.append(msg)
        last3 = last3[-3:]  # keep only the last 3
        # Newest at the top for the "falls down" feel:
        lines = []
        for idx, line in enumerate(reversed(last3)):
            if idx == 0:
                lines.append(f"- **{line}**")
            elif idx == 1:
                lines.append(f"- <span style='opacity:0.7'>{line}</span>")
            else:
                lines.append(f"- <span style='opacity:0.45'>{line}</span>")
        status_placeholder.markdown("<br/>".join(lines), unsafe_allow_html=True)

        progress = int(i * 100 / len(steps))
        progress_placeholder.progress(progress, text=f"Progress: {progress}%")
        time.sleep(delay)
    return True

def make_demo_zip() -> bytes:
    """Create a demo ZIP to download as 'phantom' result."""
    buf = io.BytesIO()
    with zipfile.ZipFile(buf, "w", compression=zipfile.ZIP_DEFLATED) as zf:
        zf.writestr("phantom/README.txt", "Demo phantom result. Replace with real generated files.")
    buf.seek(0)
    return buf.getvalue()



# ---------- Pages ----------
def page_home():
    st.subheader("Информация о контрастах и генерации фантомов")
    st.write(
        "Здесь можно разместить описание ИП (T1/T2/PD), принципы формирования данных и примеры сканов. "
        "Картинки ниже подгружаются из папки `assets/`, **автоматически центр-обрезаются в квадрат** и "
        "**приводятся к одинаковому размеру** (320×320)."
    )
    # Load 3 prepared images from assets
    images = load_and_prepare_assets("assets", count=3, size=(320, 320))
    if images:
        cols = st.columns(len(images))
        for (img, name), col in zip(images, cols):
            with col:
                st.image(img, use_container_width=False)
                # st.image(img, caption=name, use_container_width=False)
    else:
        st.info("Положите 1–3 изображения в папку `assets/` (png/jpg/tif), и они появятся здесь одинакового размера.")

    st.markdown("---")
    c1, c2 = st.columns(2)
    with c1:
        with st.container(border=True):
            st.markdown("#### 🧠 Phantom generation")
            st.write("Upload T1/T2/PD images and begin the generation.")
            st.button("Move to the phantom", type="primary", use_container_width=True, on_click=nav_to, args=("phantom",))
    with c2:
        with st.container(border=True):
            st.markdown("#### 📦 Dataset generation")
            st.write("Generation of a dataset based on pulse sequence parameters.")
            st.button("Move to the dataset", type="primary", use_container_width=True, on_click=nav_to, args=("dataset",))

def page_phantom():
    st.button("← Homepage", on_click=nav_to, args=("home",))
    st.subheader("Generate the phantom")
    st.caption("Please upload T1/T2/PD images of a brain scan")

    c1, c2, c3 = st.columns(3)
    with c1:
        t1_file = st.file_uploader("T1", type=SUPPORTED_EXTS_PHANTOM)
    with c2:
        t2_file = st.file_uploader("T2", type=SUPPORTED_EXTS_PHANTOM)
    with c3:
        pd_file = st.file_uploader("PD", type=SUPPORTED_EXTS_PHANTOM)

    start_btn = st.button("Begin generation", type="primary")
    progress_ph = st.empty()
    statuses_ph = st.empty()

    if start_btn:
        if not (t1_file and t2_file and pd_file):
            st.error("Нужно загрузить все три файла: T1, T2, PD.")
        else:
            done = run_job_stub(statuses_ph, progress_ph)
            if done:
                # Save demo result into session_state for download button
                st.session_state.phantom_blob = make_demo_zip()
                st.session_state.phantom_name = "phantom_demo.zip"
                st.success("Готово! Можно скачать результат.")

    # The download button appears only when phantom_blob is present (after job completes)
    if st.session_state.phantom_blob:
        st.download_button(
            "Download phantom",
            data=st.session_state.phantom_blob,
            file_name=st.session_state.phantom_name or "phantom_demo.zip",
            mime="application/zip",
            use_container_width=False,
            type="primary",
        )

def page_dataset():
    st.button("← Homepage", on_click=nav_to, args=("home",))
    st.subheader("Generate the dataset")
    st.caption("Dataset generation. Please choose parameters for the pulse sequence.")

    c1, c2, c3 = st.columns(3)
    with c1:
        t1d_file = st.file_uploader("T1", key="t1d", type=SUPPORTED_EXTS_PHANTOM)
    with c2:
        t2d_file = st.file_uploader("T2", key="t2d", type=SUPPORTED_EXTS_PHANTOM)
    with c3:
        pdd_file = st.file_uploader("PD", key="pdd", type=SUPPORTED_EXTS_PHANTOM)

    count = st.number_input("Сколько примеров сгенерировать", min_value=1, max_value=MAX_VALUE_DATASET, value=50, step=1)
    start_ds = st.button("Начать генерацию датасета", type="primary")
    progress2 = st.empty()
    status2 = st.empty()

    if start_ds:
        if not (t1d_file and t2d_file and pdd_file):
            st.error("Нужно загрузить все три файла: T1, T2, PD.")
        else:
            run_job_stub(status2, progress2)
            st.success(f"Датасет сформирован (демо). Количество: {int(count)}")



# ---------- Router ----------
if st.session_state.page == "home":
    page_home()
elif st.session_state.page == "phantom":
    page_phantom()
elif st.session_state.page == "dataset":
    page_dataset()
else:
    st.session_state.page = "home"
    page_home()