diff --git a/README.md b/README.md index 51f0e68..f4a44b9 100644 --- a/README.md +++ b/README.md @@ -1 +1,72 @@ -# TIFviewer-processor \ No newline at end of file +# TIFviewer-processor + +A frontend-backend separated tool for viewing and processing **16-bit grayscale TIFF** images. + +## Stack + +| Layer | Technology | +|----------|-----------------------------------------| +| Backend | Python · FastAPI · tifffile · NumPy · scikit-image · scipy | +| Frontend | Vue 3 · Vite · Chart.js · vuedraggable | + +## Features + +* Upload 16-bit TIF/TIFF files +* Grayscale histogram with hover tooltip (Value / Distribution) +* Composable enhancement pipeline (drag-to-reorder, add/remove) + * Histogram Equalization + * Local Contrast Normalization (Sigma, Epsilon, Output Gain sliders) +* Image viewer with scroll-to-zoom and drag-to-pan +* Toolbar with zoom in/out/fit and annotation-mode placeholders + +## Quick start + +### Backend + +```bash +cd backend +pip install -r requirements.txt +python main.py # starts on http://localhost:8000 +``` + +### Frontend + +```bash +cd frontend +npm install +npm run dev # starts on http://localhost:5173 +``` + +Open **http://localhost:5173** in your browser. The Vite dev-server proxies +all `/api/*` requests to the FastAPI backend automatically. + +## API reference + +| Method | Path | Description | +|--------|------|-------------| +| `POST` | `/api/upload` | Upload a `.tif`/`.tiff` file; returns `file_id` | +| `GET` | `/api/image/{file_id}` | Render processed PNG (query: `enhancements`, `min_val`, `max_val`) | +| `GET` | `/api/histogram/{file_id}` | 256-bin histogram JSON | +| `POST` | `/api/process` | Apply pipeline; returns base64 PNG + histogram | + +## Project layout + +``` +backend/ + main.py FastAPI application + requirements.txt + processors/ + histogram_eq.py Histogram equalization + local_contrast_norm.py Local contrast normalization +frontend/ + src/ + App.vue Root component / layout + components/ + Histogram.vue Chart.js histogram panel + EnhancementPanel.vue Pipeline list (drag-and-drop) + ParameterPanel.vue Slider controls + SliderRow.vue Single slider with value display + ImageViewer.vue Pan / zoom image display + Toolbar.vue File open + zoom + annotation toolbar + vite.config.js Proxies /api → localhost:8000 +``` diff --git a/backend/.gitignore b/backend/.gitignore new file mode 100644 index 0000000..a5f8b9d --- /dev/null +++ b/backend/.gitignore @@ -0,0 +1,6 @@ +__pycache__/ +*.py[cod] +*.egg-info/ +.env +.venv/ +venv/ diff --git a/backend/main.py b/backend/main.py new file mode 100644 index 0000000..3a31b52 --- /dev/null +++ b/backend/main.py @@ -0,0 +1,150 @@ +import io +import json +import uuid +import base64 +from typing import Any, Optional + +import numpy as np +import tifffile +from PIL import Image +from fastapi import FastAPI, File, HTTPException, UploadFile +from fastapi.middleware.cors import CORSMiddleware +from fastapi.responses import JSONResponse, Response +from pydantic import BaseModel + +from processors import PROCESSORS + +app = FastAPI(title="TIF Viewer API") + +app.add_middleware( + CORSMiddleware, + allow_origins=["*"], + allow_credentials=True, + allow_methods=["*"], + allow_headers=["*"], +) + +# In-memory store: file_id -> numpy array (float32, range 0-65535). +# Replace with a persistent cache (e.g. Redis / disk) for production use. +image_store: dict[str, np.ndarray] = {} + + +# ── Helpers ─────────────────────────────────────────────────────────────────── + +def _apply_pipeline(image: np.ndarray, enhancements: list[dict]) -> np.ndarray: + """Apply a list of {type, params} dicts sequentially.""" + result = image.copy() + for enh in enhancements: + enh_type = enh.get("type") + params = enh.get("params") or {} + processor = PROCESSORS.get(enh_type) + if processor is None: + raise HTTPException(status_code=400, detail=f"Unknown enhancement: {enh_type!r}") + result = processor(result, **params) + return result + + +def _to_png_bytes( + image: np.ndarray, + min_val: Optional[float], + max_val: Optional[float], +) -> bytes: + """Normalise to 8-bit and encode as PNG.""" + img = image.astype(np.float32) + lo = float(min_val) if min_val is not None else float(img.min()) + hi = float(max_val) if max_val is not None else float(img.max()) + if hi == lo: + hi = lo + 1.0 + img_8 = ((img - lo) / (hi - lo) * 255.0).clip(0, 255).astype(np.uint8) + buf = io.BytesIO() + Image.fromarray(img_8, mode="L").save(buf, format="PNG") + return buf.getvalue() + + +def _compute_histogram(image: np.ndarray) -> dict: + """256-bin histogram over [0, 65535].""" + counts, edges = np.histogram(image, bins=256, range=(0, 65535)) + bins = ((edges[:-1] + edges[1:]) / 2.0).astype(int).tolist() + return {"bins": bins, "counts": counts.tolist()} + + +# ── Endpoints ───────────────────────────────────────────────────────────────── + +@app.get("/") +def root(): + return {"status": "ok", "message": "TIF Viewer API"} + + +@app.post("/api/upload") +async def upload_file(file: UploadFile = File(...)): + if not file.filename.lower().endswith((".tif", ".tiff")): + raise HTTPException(status_code=400, detail="Only .tif / .tiff files are accepted") + + data = await file.read() + try: + img = tifffile.imread(io.BytesIO(data)) + except Exception as exc: + raise HTTPException(status_code=400, detail=f"Failed to read TIFF: {exc}") + + # Flatten to 2-D grayscale + if img.ndim == 3: + img = img[..., 0] if img.shape[2] == 1 else img.mean(axis=2) + elif img.ndim != 2: + raise HTTPException(status_code=400, detail="Unsupported TIFF dimensionality") + + img = img.astype(np.float32) + + file_id = str(uuid.uuid4()) + image_store[file_id] = img + return {"file_id": file_id, "width": int(img.shape[1]), "height": int(img.shape[0])} + + +@app.get("/api/image/{file_id}") +def get_image( + file_id: str, + enhancements: Optional[str] = None, + min_val: Optional[float] = None, + max_val: Optional[float] = None, +): + if file_id not in image_store: + raise HTTPException(status_code=404, detail="File not found") + + img = image_store[file_id] + + if enhancements: + try: + enh_list = json.loads(enhancements) + except json.JSONDecodeError: + raise HTTPException(status_code=400, detail="Invalid enhancements JSON") + img = _apply_pipeline(img, enh_list) + + return Response(content=_to_png_bytes(img, min_val, max_val), media_type="image/png") + + +@app.get("/api/histogram/{file_id}") +def get_histogram(file_id: str): + if file_id not in image_store: + raise HTTPException(status_code=404, detail="File not found") + return JSONResponse(_compute_histogram(image_store[file_id])) + + +class ProcessRequest(BaseModel): + file_id: str + enhancements: list[dict[str, Any]] = [] + min_val: Optional[float] = None + max_val: Optional[float] = None + + +@app.post("/api/process") +def process_image(req: ProcessRequest): + if req.file_id not in image_store: + raise HTTPException(status_code=404, detail="File not found") + + img = _apply_pipeline(image_store[req.file_id], req.enhancements) + b64 = base64.b64encode(_to_png_bytes(img, req.min_val, req.max_val)).decode() + return {"image": b64, "histogram": _compute_histogram(img)} + + +if __name__ == "__main__": + import uvicorn + uvicorn.run("main:app", host="0.0.0.0", port=8000, reload=False) diff --git a/backend/processors/__init__.py b/backend/processors/__init__.py new file mode 100644 index 0000000..d878f08 --- /dev/null +++ b/backend/processors/__init__.py @@ -0,0 +1,9 @@ +from processors.histogram_eq import apply as _hist_eq +from processors.local_contrast_norm import apply as _lcn + +PROCESSORS = { + "histogram_equalization": _hist_eq, + "local_contrast_normalization": _lcn, +} + +__all__ = ["PROCESSORS"] diff --git a/backend/processors/histogram_eq.py b/backend/processors/histogram_eq.py new file mode 100644 index 0000000..5244e75 --- /dev/null +++ b/backend/processors/histogram_eq.py @@ -0,0 +1,14 @@ +import numpy as np +from skimage.exposure import equalize_hist + + +def apply(image: np.ndarray) -> np.ndarray: + """Histogram equalization on a 16-bit grayscale image. + + The image is normalised to [0, 1] before equalisation, then scaled back + to the uint16 range so that downstream processors continue to work on a + consistent data type. + """ + img_float = image.astype(np.float32) / 65535.0 + equalised = equalize_hist(img_float) # returns float in [0, 1] + return (equalised * 65535.0).astype(np.float32) diff --git a/backend/processors/local_contrast_norm.py b/backend/processors/local_contrast_norm.py new file mode 100644 index 0000000..09bb611 --- /dev/null +++ b/backend/processors/local_contrast_norm.py @@ -0,0 +1,41 @@ +import numpy as np +from scipy.ndimage import gaussian_filter + + +def apply( + image: np.ndarray, + sigma: float = 25.54, + epsilon: float = 0.08, + output_gain: float = 1.0, +) -> np.ndarray: + """Local contrast normalization. + + For each pixel p: + p_norm = (p - local_mean) / (local_std + epsilon) + + Parameters + ---------- + image: Input 2-D array (uint16 or float32). + sigma: Gaussian blur radius for computing local statistics. + epsilon: Stability constant added to the local standard deviation. + output_gain: Multiplicative gain applied to the normalised image before + rescaling back to the uint16 range. + """ + img = image.astype(np.float32) + + local_mean = gaussian_filter(img, sigma=sigma) + local_mean_sq = gaussian_filter(img ** 2, sigma=sigma) + local_var = np.maximum(local_mean_sq - local_mean ** 2, 0.0) + local_std = np.sqrt(local_var) + + normalised = (img - local_mean) / (local_std + epsilon) + normalised *= output_gain + + # Rescale to [0, 65535] for consistency with the rest of the pipeline + lo, hi = normalised.min(), normalised.max() + if hi > lo: + normalised = (normalised - lo) / (hi - lo) * 65535.0 + else: + normalised = np.zeros_like(normalised) + + return normalised.astype(np.float32) diff --git a/backend/requirements.txt b/backend/requirements.txt new file mode 100644 index 0000000..7d164d0 --- /dev/null +++ b/backend/requirements.txt @@ -0,0 +1,8 @@ +fastapi>=0.110.0 +uvicorn[standard]>=0.29.0 +python-multipart>=0.0.9 +numpy>=1.26.0 +tifffile>=2024.2.12 +Pillow>=10.3.0 +scikit-image>=0.22.0 +scipy>=1.13.0 diff --git a/frontend/.gitignore b/frontend/.gitignore new file mode 100644 index 0000000..a547bf3 --- /dev/null +++ b/frontend/.gitignore @@ -0,0 +1,24 @@ +# Logs +logs +*.log +npm-debug.log* +yarn-debug.log* +yarn-error.log* +pnpm-debug.log* +lerna-debug.log* + +node_modules +dist +dist-ssr +*.local + +# Editor directories and files +.vscode/* +!.vscode/extensions.json +.idea +.DS_Store +*.suo +*.ntvs* +*.njsproj +*.sln +*.sw? diff --git a/frontend/.vscode/extensions.json b/frontend/.vscode/extensions.json new file mode 100644 index 0000000..a7cea0b --- /dev/null +++ b/frontend/.vscode/extensions.json @@ -0,0 +1,3 @@ +{ + "recommendations": ["Vue.volar"] +} diff --git a/frontend/README.md b/frontend/README.md new file mode 100644 index 0000000..1511959 --- /dev/null +++ b/frontend/README.md @@ -0,0 +1,5 @@ +# Vue 3 + Vite + +This template should help get you started developing with Vue 3 in Vite. 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a/frontend/public/icons.svg b/frontend/public/icons.svg new file mode 100644 index 0000000..e952219 --- /dev/null +++ b/frontend/public/icons.svg @@ -0,0 +1,24 @@ + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/frontend/src/App.vue b/frontend/src/App.vue new file mode 100644 index 0000000..57fa839 --- /dev/null +++ b/frontend/src/App.vue @@ -0,0 +1,192 @@ + + + + + diff --git a/frontend/src/assets/hero.png b/frontend/src/assets/hero.png new file mode 100644 index 0000000..cc51a3d Binary files /dev/null and b/frontend/src/assets/hero.png differ diff --git a/frontend/src/assets/vite.svg b/frontend/src/assets/vite.svg new file mode 100644 index 0000000..5101b67 --- /dev/null +++ b/frontend/src/assets/vite.svg @@ -0,0 +1 @@ +Vite diff --git a/frontend/src/assets/vue.svg b/frontend/src/assets/vue.svg new file mode 100644 index 0000000..770e9d3 --- /dev/null +++ b/frontend/src/assets/vue.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/frontend/src/components/EnhancementPanel.vue b/frontend/src/components/EnhancementPanel.vue new file mode 100644 index 0000000..ade5d19 --- /dev/null +++ b/frontend/src/components/EnhancementPanel.vue @@ -0,0 +1,138 @@ + + + + + diff --git a/frontend/src/components/HelloWorld.vue b/frontend/src/components/HelloWorld.vue new file mode 100644 index 0000000..3a7b808 --- /dev/null +++ b/frontend/src/components/HelloWorld.vue @@ -0,0 +1,93 @@ + + + diff --git a/frontend/src/components/Histogram.vue b/frontend/src/components/Histogram.vue new file mode 100644 index 0000000..4395693 --- /dev/null +++ b/frontend/src/components/Histogram.vue @@ -0,0 +1,116 @@ + + + + + diff --git a/frontend/src/components/ImageViewer.vue b/frontend/src/components/ImageViewer.vue new file mode 100644 index 0000000..53b5361 --- /dev/null +++ b/frontend/src/components/ImageViewer.vue @@ -0,0 +1,137 @@ + + + + + diff --git a/frontend/src/components/ParameterPanel.vue b/frontend/src/components/ParameterPanel.vue new file mode 100644 index 0000000..a2245a2 --- /dev/null +++ b/frontend/src/components/ParameterPanel.vue @@ -0,0 +1,74 @@ + + + + + diff --git a/frontend/src/components/SliderRow.vue b/frontend/src/components/SliderRow.vue new file mode 100644 index 0000000..5ac675f --- /dev/null +++ b/frontend/src/components/SliderRow.vue @@ -0,0 +1,89 @@ + + + + + diff --git a/frontend/src/components/Toolbar.vue b/frontend/src/components/Toolbar.vue new file mode 100644 index 0000000..525820d --- /dev/null +++ b/frontend/src/components/Toolbar.vue @@ -0,0 +1,105 @@ + + + + + diff --git a/frontend/src/main.js b/frontend/src/main.js new file mode 100644 index 0000000..2425c0f --- /dev/null +++ b/frontend/src/main.js @@ -0,0 +1,5 @@ +import { createApp } from 'vue' +import './style.css' +import App from './App.vue' + +createApp(App).mount('#app') diff --git a/frontend/src/style.css b/frontend/src/style.css new file mode 100644 index 0000000..2ed1476 --- /dev/null +++ b/frontend/src/style.css @@ -0,0 +1,21 @@ +*, *::before, *::after { box-sizing: border-box; margin: 0; padding: 0; } + +body { + font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, sans-serif; + background: #f5f5f5; + color: #333; + height: 100vh; + overflow: hidden; +} + +#app { height: 100vh; display: flex; flex-direction: column; } + +button { + cursor: pointer; + border: none; + background: none; + font-size: 14px; +} +button:hover { opacity: 0.7; } + +input[type=range] { width: 100%; cursor: pointer; } diff --git a/frontend/vite.config.js b/frontend/vite.config.js new file mode 100644 index 0000000..84c9560 --- /dev/null +++ b/frontend/vite.config.js @@ -0,0 +1,14 @@ +import { defineConfig } from 'vite' +import vue from '@vitejs/plugin-vue' + +export default defineConfig({ + plugins: [vue()], + server: { + proxy: { + '/api': { + target: 'http://localhost:8000', + changeOrigin: true, + }, + }, + }, +})