Commit ·
8a7a521
1
Parent(s): 19d1ea6
Add CLI support for microscopy image enhancement and update README
Browse files- README.md +41 -1
- app.py +143 -72
- enhance_cli.py +369 -0
README.md
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An AI-powered microscopy image enhancement tool using the FLUX.2 model. This application provides intelligent image enhancement while preserving cellular structures and fine details.
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## ✨ Features
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- **Batch Processing**: Process multiple images at once or entire archived folders
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# Install dependencies
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pip install -r requirements.txt
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# Run the
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python app.py
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```
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## 📋 Requirements
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- Python 3.8+
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An AI-powered microscopy image enhancement tool using the FLUX.2 model. This application provides intelligent image enhancement while preserving cellular structures and fine details.
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**Available in two versions:**
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- 🌐 **Web UI** (Gradio): Interactive web interface with drag-and-drop support
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- ⌨️ **CLI** (Command Line): Batch processing tool for automation and scripting
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## ✨ Features
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- **Batch Processing**: Process multiple images at once or entire archived folders
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# Install dependencies
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pip install -r requirements.txt
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# Run the web UI
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python app.py
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# Or use the CLI version
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python enhance_cli.py -i input.jpg -o output/
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```
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## ⌨️ CLI Usage
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For batch processing and automation, use the command-line interface:
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```bash
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# Basic usage
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python enhance_cli.py -i input.jpg -o output/
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# Process multiple images
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python enhance_cli.py -i img1.jpg img2.png img3.tif -o output/
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# Process entire directory (recursive)
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python enhance_cli.py -i images_folder/ -o output/
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# Custom parameters
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python enhance_cli.py -i input.jpg -o output/ \
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--guidance-scale 3.0 \
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--steps 40 \
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--prompt "enhance cellular structure"
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# Quiet mode (minimal output)
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python enhance_cli.py -i input.jpg -o output/ --quiet
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```
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### CLI Arguments
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- `-i, --input`: Input path(s) - image files or directories (required)
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- `-o, --output`: Output directory for enhanced images (required)
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- `-p, --prompt`: Enhancement prompt (optional)
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- `-g, --guidance-scale`: Guidance scale 1.0-5.0 (default: 2.0)
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- `-s, --steps`: Inference steps 10-50 (default: 30)
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- `-q, --quiet`: Quiet mode - minimal output
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## 📋 Requirements
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- Python 3.8+
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app.py
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import gradio as gr
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import torch
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import
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from diffusers import Flux2Pipeline
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from diffusers.utils import load_image
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from pathlib import Path
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from PIL import Image
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import os
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import zipfile
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import py7zr
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import tempfile
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import shutil
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import numpy as np
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from skimage.metrics import peak_signal_noise_ratio, structural_similarity
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from skimage.util import img_as_float
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# =========================
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# Config
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# =========================
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MODEL_ID = "diffusers/FLUX.2-dev-bnb-4bit"
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TORCH_DTYPE = torch.bfloat16
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# =========================
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-
#
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# =========================
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_pipe = None
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def _get_pipe():
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"""
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Lazy-load the pipeline
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"""
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global _pipe
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if _pipe is None:
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if not torch.cuda.is_available():
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# On ZeroGPU startup this is False; inside @spaces.GPU it should become True
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raise RuntimeError(
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"No GPU
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"On HF ZeroGPU you must only load the bnb-4bit model inside a @spaces.GPU function."
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)
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_pipe = Flux2Pipeline.from_pretrained(
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MODEL_ID,
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torch_dtype=TORCH_DTYPE,
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# removed fix_mistral_regex=True (it was ignored for Flux2Pipeline)
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)
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_pipe.to("cuda")
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return _pipe
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@
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def process_images(files, prompt, guidance_scale, num_steps, progress=gr.Progress()):
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"""
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Process uploaded files (images or archives) and return:
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- gallery preview (first 10 pairs)
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- summary text
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"""
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if not files:
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return
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if not prompt or prompt.strip() == "":
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prompt = DEFAULT_PROMPT
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guidance_scale = float(guidance_scale)
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num_steps = int(num_steps)
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# Temp
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temp_dir = tempfile.mkdtemp(prefix="flux_in_")
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-
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try:
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progress(0.0, desc="Preparing files...")
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file_ext = Path(file_path).suffix.lower()
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if file_ext in [".zip", ".7z"]:
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progress(0.05, desc=f"Extracting: {Path(file_path).name} ...")
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extract_dir = os.path.join(temp_dir, Path(file_path).stem)
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os.makedirs(extract_dir, exist_ok=True)
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all_images.append((file_path, Path(file_path).name, None))
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if not all_images:
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return
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total_images = len(all_images)
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progress(0.10, desc=f"Found {total_images} images. Loading model...")
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# Load pipeline
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pipe = _get_pipe()
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results = []
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desc=f"Processing {idx+1}/{total_images}: {Path(img_path).name}",
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)
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# Load input image
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input_image = load_image(img_path)
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# Run inference
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enhanced_image = pipe(
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image=input_image,
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prompt=prompt,
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num_inference_steps=num_steps,
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).images[0]
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# Metrics
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psnr, ssim = calculate_psnr_ssim(input_image, enhanced_image)
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#
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output_rel_path = rel_path
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else:
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output_rel_path = rel_path
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out_path = os.path.join(output_dir, output_rel_path)
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os.makedirs(os.path.dirname(out_path), exist_ok=True)
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"ssim": ssim,
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}
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)
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metrics_lines.append(
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f"{output_rel_path}: PSNR={psnr:.2f} dB, SSIM={ssim:.4f}"
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)
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progress(0.92, desc="Packaging ZIP...")
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-
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# Create output zip
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output_zip_path = os.path.join(
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tempfile.gettempdir(), "enhanced_images_flux.zip"
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)
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with zipfile.ZipFile(output_zip_path, "w", zipfile.ZIP_DEFLATED) as zipf:
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for root, _, fs in os.walk(output_dir):
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for f in fs:
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fp = os.path.join(root, f)
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arcname = os.path.relpath(fp, output_dir)
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zipf.write(fp, arcname)
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avg_psnr = float(np.mean([r["psnr"] for r in results])) if results else 0.0
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avg_ssim = float(np.mean([r["ssim"] for r in results])) if results else 0.0
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summary = (
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"✅ Processing completed!\n\n"
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f"Total images processed: {total_images}\n"
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f"Average PSNR: {avg_psnr:.2f} dB\n"
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f"Average SSIM: {avg_ssim:.4f}\n\n"
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"Individual metrics:\n" + "\n".join(metrics_lines)
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)
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# Build gallery preview (first 10 results ->
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gallery_images = []
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for r in results[:10]:
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gallery_images.append((r["original"], f"Original: {r['filename']}"))
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)
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)
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except Exception as e:
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return
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finally:
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# Cleanup temp
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if os.path.exists(temp_dir):
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shutil.rmtree(temp_dir, ignore_errors=True)
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if os.path.exists(output_dir):
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shutil.rmtree(output_dir, ignore_errors=True)
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# =========================
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# =========================
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with gr.Blocks(title="Flux Microscopy Image Enhancement") as demo:
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gr.Markdown(
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"""
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# 🔬 Flux Microscopy Image Enhancement
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Upload microscopy images (individual files or compressed archives) for AI-powered enhancement.
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- Images: JPG, PNG, BMP, TIFF
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- Archives: ZIP, 7Z (will process all images inside)
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**
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"""
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)
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process_btn = gr.Button("🚀 Enhance Images", variant="primary", size="lg")
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gr.Markdown("### Example")
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gr.Examples(
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examples=[
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[None, DEFAULT_PROMPT, GUIDANCE_SCALE, NUM_INFERENCE_STEPS],
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],
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inputs=[
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file_input,
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prompt_input,
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guidance_scale_input,
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num_steps_input,
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],
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)
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with gr.Column(scale=2):
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gallery_output = gr.Gallery(
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label="Results Preview (Original vs Enhanced)",
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object_fit="contain",
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)
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-
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summary_output = gr.Textbox(
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label="Processing Summary & Metrics",
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process_btn.click(
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fn=process_images,
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inputs=[file_input, prompt_input, guidance_scale_input, num_steps_input],
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outputs=[gallery_output,
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)
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gr.Markdown(
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- **Inference Steps**: 30 (balanced quality and speed)
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### Quality Metrics
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- **PSNR** (Peak Signal-to-Noise Ratio): Higher is better
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- **SSIM** (Structural Similarity Index): Closer to 1.0 is better
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"""
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)
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import os
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import zipfile
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import tempfile
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import shutil
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import uuid
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from pathlib import Path
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import gradio as gr
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import torch
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import numpy as np
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from PIL import Image
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from diffusers import Flux2Pipeline
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from diffusers.utils import load_image
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import py7zr
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from skimage.metrics import peak_signal_noise_ratio, structural_similarity
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from skimage.util import img_as_float
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+
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# =========================
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# Config
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# =========================
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MODEL_ID = "diffusers/FLUX.2-dev-bnb-4bit"
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TORCH_DTYPE = torch.bfloat16
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# =========================
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# HF Spaces env detection + safe "spaces" decorator
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# =========================
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def _is_hf_space_env() -> bool:
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"""
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Detect whether we're running on Hugging Face Spaces runtime.
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Common env vars present in Spaces:
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- SPACE_ID
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- HF_SPACE_ID
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- SYSTEM=spaces
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"""
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return any(os.getenv(k) for k in ("SPACE_ID", "HF_SPACE_ID")) or (
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| 54 |
+
os.getenv("SYSTEM", "").lower() == "spaces"
|
| 55 |
+
)
|
| 56 |
+
|
| 57 |
+
|
| 58 |
+
IS_HF_SPACES = _is_hf_space_env()
|
| 59 |
+
|
| 60 |
+
try:
|
| 61 |
+
import spaces # available on HF Spaces
|
| 62 |
+
except Exception:
|
| 63 |
+
spaces = None
|
| 64 |
+
|
| 65 |
+
|
| 66 |
+
def gpu_decorator(duration: int = 180):
|
| 67 |
+
"""
|
| 68 |
+
If on HF Spaces and spaces.GPU exists -> use it.
|
| 69 |
+
Else -> no-op decorator (local runs normally, using local GPU if available).
|
| 70 |
+
"""
|
| 71 |
+
if IS_HF_SPACES and (spaces is not None) and hasattr(spaces, "GPU"):
|
| 72 |
+
return spaces.GPU(duration=duration)
|
| 73 |
+
|
| 74 |
+
def _noop(fn):
|
| 75 |
+
return fn
|
| 76 |
+
|
| 77 |
+
return _noop
|
| 78 |
+
|
| 79 |
+
|
| 80 |
+
# =========================
|
| 81 |
+
# Global cached pipeline
|
| 82 |
# =========================
|
| 83 |
_pipe = None
|
| 84 |
|
|
|
|
| 133 |
|
| 134 |
def _get_pipe():
|
| 135 |
"""
|
| 136 |
+
Lazy-load the pipeline.
|
| 137 |
+
- On HF Spaces ZeroGPU: MUST be called inside a @spaces.GPU runtime (gpu_decorator handles this).
|
| 138 |
+
- Locally: will use local GPU.
|
| 139 |
"""
|
| 140 |
global _pipe
|
| 141 |
|
| 142 |
if _pipe is None:
|
| 143 |
if not torch.cuda.is_available():
|
|
|
|
| 144 |
raise RuntimeError(
|
| 145 |
+
"No CUDA GPU detected. This 4-bit bnb model requires GPU to load/run."
|
|
|
|
| 146 |
)
|
| 147 |
|
| 148 |
_pipe = Flux2Pipeline.from_pretrained(
|
| 149 |
MODEL_ID,
|
| 150 |
torch_dtype=TORCH_DTYPE,
|
|
|
|
| 151 |
)
|
| 152 |
_pipe.to("cuda")
|
| 153 |
|
| 154 |
return _pipe
|
| 155 |
|
| 156 |
|
| 157 |
+
@gpu_decorator(duration=180)
|
| 158 |
def process_images(files, prompt, guidance_scale, num_steps, progress=gr.Progress()):
|
| 159 |
"""
|
| 160 |
Process uploaded files (images or archives) and return:
|
| 161 |
- gallery preview (first 10 pairs)
|
| 162 |
+
- files download (when only images uploaded)
|
| 163 |
+
- zip download (when archive uploaded)
|
| 164 |
- summary text
|
| 165 |
"""
|
| 166 |
if not files:
|
| 167 |
+
return (
|
| 168 |
+
None,
|
| 169 |
+
gr.update(value=None, visible=False),
|
| 170 |
+
gr.update(value=None, visible=False),
|
| 171 |
+
"Please upload at least one file.",
|
| 172 |
+
)
|
| 173 |
|
| 174 |
if not prompt or prompt.strip() == "":
|
| 175 |
prompt = DEFAULT_PROMPT
|
|
|
|
| 177 |
guidance_scale = float(guidance_scale)
|
| 178 |
num_steps = int(num_steps)
|
| 179 |
|
| 180 |
+
# Temp for extraction / staging input
|
| 181 |
temp_dir = tempfile.mkdtemp(prefix="flux_in_")
|
| 182 |
+
|
| 183 |
+
# IMPORTANT:
|
| 184 |
+
# Result files MUST remain on disk for Gradio download.
|
| 185 |
+
# So we create a persistent temp dir and DO NOT delete it in finally.
|
| 186 |
+
run_id = uuid.uuid4().hex[:10]
|
| 187 |
+
output_dir = tempfile.mkdtemp(prefix=f"flux_results_{run_id}_")
|
| 188 |
+
|
| 189 |
+
has_archive = False
|
| 190 |
|
| 191 |
try:
|
| 192 |
progress(0.0, desc="Preparing files...")
|
|
|
|
| 197 |
file_ext = Path(file_path).suffix.lower()
|
| 198 |
|
| 199 |
if file_ext in [".zip", ".7z"]:
|
| 200 |
+
has_archive = True
|
| 201 |
progress(0.05, desc=f"Extracting: {Path(file_path).name} ...")
|
| 202 |
extract_dir = os.path.join(temp_dir, Path(file_path).stem)
|
| 203 |
os.makedirs(extract_dir, exist_ok=True)
|
|
|
|
| 212 |
all_images.append((file_path, Path(file_path).name, None))
|
| 213 |
|
| 214 |
if not all_images:
|
| 215 |
+
return (
|
| 216 |
+
None,
|
| 217 |
+
gr.update(value=None, visible=False),
|
| 218 |
+
gr.update(value=None, visible=False),
|
| 219 |
+
"No valid images found in uploaded files.",
|
| 220 |
+
)
|
| 221 |
|
| 222 |
total_images = len(all_images)
|
| 223 |
progress(0.10, desc=f"Found {total_images} images. Loading model...")
|
| 224 |
|
| 225 |
+
# Load pipeline (inside GPU runtime on Spaces; local GPU otherwise)
|
| 226 |
pipe = _get_pipe()
|
| 227 |
|
| 228 |
results = []
|
|
|
|
| 236 |
desc=f"Processing {idx+1}/{total_images}: {Path(img_path).name}",
|
| 237 |
)
|
| 238 |
|
|
|
|
| 239 |
input_image = load_image(img_path)
|
| 240 |
|
|
|
|
| 241 |
enhanced_image = pipe(
|
| 242 |
image=input_image,
|
| 243 |
prompt=prompt,
|
|
|
|
| 245 |
num_inference_steps=num_steps,
|
| 246 |
).images[0]
|
| 247 |
|
|
|
|
| 248 |
psnr, ssim = calculate_psnr_ssim(input_image, enhanced_image)
|
| 249 |
|
| 250 |
+
# Preserve structure if from archive
|
| 251 |
+
output_rel_path = rel_path
|
|
|
|
|
|
|
|
|
|
| 252 |
|
| 253 |
out_path = os.path.join(output_dir, output_rel_path)
|
| 254 |
os.makedirs(os.path.dirname(out_path), exist_ok=True)
|
|
|
|
| 269 |
"ssim": ssim,
|
| 270 |
}
|
| 271 |
)
|
| 272 |
+
|
| 273 |
metrics_lines.append(
|
| 274 |
f"{output_rel_path}: PSNR={psnr:.2f} dB, SSIM={ssim:.4f}"
|
| 275 |
)
|
| 276 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 277 |
avg_psnr = float(np.mean([r["psnr"] for r in results])) if results else 0.0
|
| 278 |
avg_ssim = float(np.mean([r["ssim"] for r in results])) if results else 0.0
|
| 279 |
|
| 280 |
summary = (
|
| 281 |
"✅ Processing completed!\n\n"
|
| 282 |
+
f"Environment: {'Hugging Face Spaces' if IS_HF_SPACES else 'Local'}\n"
|
| 283 |
+
f"GPU available: {torch.cuda.is_available()}\n\n"
|
| 284 |
f"Total images processed: {total_images}\n"
|
| 285 |
f"Average PSNR: {avg_psnr:.2f} dB\n"
|
| 286 |
f"Average SSIM: {avg_ssim:.4f}\n\n"
|
| 287 |
"Individual metrics:\n" + "\n".join(metrics_lines)
|
| 288 |
)
|
| 289 |
|
| 290 |
+
# Build gallery preview (first 10 results -> original+enhanced)
|
| 291 |
gallery_images = []
|
| 292 |
for r in results[:10]:
|
| 293 |
gallery_images.append((r["original"], f"Original: {r['filename']}"))
|
|
|
|
| 298 |
)
|
| 299 |
)
|
| 300 |
|
| 301 |
+
# Decide download output:
|
| 302 |
+
# - If user uploaded any archive -> provide ZIP
|
| 303 |
+
# - Else -> provide enhanced files directly
|
| 304 |
+
if has_archive:
|
| 305 |
+
progress(0.92, desc="Packaging ZIP...")
|
| 306 |
+
|
| 307 |
+
output_zip_path = os.path.join(
|
| 308 |
+
tempfile.gettempdir(), f"enhanced_images_flux_{run_id}.zip"
|
| 309 |
+
)
|
| 310 |
+
|
| 311 |
+
with zipfile.ZipFile(output_zip_path, "w", zipfile.ZIP_DEFLATED) as zipf:
|
| 312 |
+
for root, _, fs in os.walk(output_dir):
|
| 313 |
+
for f in fs:
|
| 314 |
+
fp = os.path.join(root, f)
|
| 315 |
+
arcname = os.path.relpath(fp, output_dir)
|
| 316 |
+
zipf.write(fp, arcname)
|
| 317 |
+
|
| 318 |
+
progress(1.0, desc="Done!")
|
| 319 |
+
return (
|
| 320 |
+
gallery_images,
|
| 321 |
+
gr.update(value=None, visible=False), # files hidden
|
| 322 |
+
gr.update(value=output_zip_path, visible=True), # zip shown
|
| 323 |
+
summary,
|
| 324 |
+
)
|
| 325 |
+
else:
|
| 326 |
+
enhanced_paths = [r["output_path"] for r in results]
|
| 327 |
+
progress(1.0, desc="Done!")
|
| 328 |
+
return (
|
| 329 |
+
gallery_images,
|
| 330 |
+
gr.update(value=enhanced_paths, visible=True), # files shown
|
| 331 |
+
gr.update(value=None, visible=False), # zip hidden
|
| 332 |
+
summary,
|
| 333 |
+
)
|
| 334 |
|
| 335 |
except Exception as e:
|
| 336 |
+
return (
|
| 337 |
+
None,
|
| 338 |
+
gr.update(value=None, visible=False),
|
| 339 |
+
gr.update(value=None, visible=False),
|
| 340 |
+
f"Error during processing: {str(e)}",
|
| 341 |
+
)
|
| 342 |
|
| 343 |
finally:
|
| 344 |
+
# Cleanup ONLY input/extraction temp dir.
|
| 345 |
+
# DO NOT delete output_dir because Gradio downloads need the files to remain.
|
| 346 |
if os.path.exists(temp_dir):
|
| 347 |
shutil.rmtree(temp_dir, ignore_errors=True)
|
|
|
|
|
|
|
| 348 |
|
| 349 |
|
| 350 |
# =========================
|
|
|
|
| 352 |
# =========================
|
| 353 |
with gr.Blocks(title="Flux Microscopy Image Enhancement") as demo:
|
| 354 |
gr.Markdown(
|
| 355 |
+
f"""
|
| 356 |
# 🔬 Flux Microscopy Image Enhancement
|
| 357 |
|
| 358 |
Upload microscopy images (individual files or compressed archives) for AI-powered enhancement.
|
|
|
|
| 361 |
- Images: JPG, PNG, BMP, TIFF
|
| 362 |
- Archives: ZIP, 7Z (will process all images inside)
|
| 363 |
|
| 364 |
+
**Download behavior:**
|
| 365 |
+
- If you upload **only images** → you can download the enhanced **image files directly** (`*_flux` suffix)
|
| 366 |
+
- If you upload **a ZIP/7Z** → you can download **one ZIP** (images inside use `*_flux` suffix)
|
| 367 |
+
|
| 368 |
+
**Runtime detection:**
|
| 369 |
+
- Detected environment: **{"Hugging Face Spaces" if IS_HF_SPACES else "Local"}**
|
| 370 |
"""
|
| 371 |
)
|
| 372 |
|
|
|
|
| 407 |
|
| 408 |
process_btn = gr.Button("🚀 Enhance Images", variant="primary", size="lg")
|
| 409 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 410 |
with gr.Column(scale=2):
|
| 411 |
gallery_output = gr.Gallery(
|
| 412 |
label="Results Preview (Original vs Enhanced)",
|
|
|
|
| 416 |
object_fit="contain",
|
| 417 |
)
|
| 418 |
|
| 419 |
+
files_output = gr.Files(
|
| 420 |
+
label="📥 Download Enhanced Images (Files)", visible=False
|
| 421 |
+
)
|
| 422 |
+
zip_output = gr.File(
|
| 423 |
+
label="📥 Download Enhanced Images (ZIP)", visible=False
|
| 424 |
+
)
|
| 425 |
|
| 426 |
summary_output = gr.Textbox(
|
| 427 |
label="Processing Summary & Metrics",
|
|
|
|
| 432 |
process_btn.click(
|
| 433 |
fn=process_images,
|
| 434 |
inputs=[file_input, prompt_input, guidance_scale_input, num_steps_input],
|
| 435 |
+
outputs=[gallery_output, files_output, zip_output, summary_output],
|
| 436 |
)
|
| 437 |
|
| 438 |
gr.Markdown(
|
|
|
|
| 443 |
- **Inference Steps**: 30 (balanced quality and speed)
|
| 444 |
|
| 445 |
### Quality Metrics
|
| 446 |
+
- **PSNR** (Peak Signal-to-Noise Ratio): Higher is better
|
| 447 |
+
- **SSIM** (Structural Similarity Index): Closer to 1.0 is better
|
| 448 |
"""
|
| 449 |
)
|
| 450 |
|
enhance_cli.py
ADDED
|
@@ -0,0 +1,369 @@
|
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|
| 1 |
+
#!/usr/bin/env python3
|
| 2 |
+
"""
|
| 3 |
+
Flux Microscopy Image Enhancement - Command Line Interface
|
| 4 |
+
Process microscopy images with AI-powered enhancement using argparse for all parameters
|
| 5 |
+
"""
|
| 6 |
+
|
| 7 |
+
import argparse
|
| 8 |
+
import torch
|
| 9 |
+
from diffusers import Flux2Pipeline
|
| 10 |
+
from diffusers.utils import load_image
|
| 11 |
+
from pathlib import Path
|
| 12 |
+
from PIL import Image
|
| 13 |
+
import os
|
| 14 |
+
import shutil
|
| 15 |
+
import numpy as np
|
| 16 |
+
from skimage.metrics import peak_signal_noise_ratio, structural_similarity
|
| 17 |
+
from skimage.util import img_as_float
|
| 18 |
+
import sys
|
| 19 |
+
from typing import List, Tuple
|
| 20 |
+
|
| 21 |
+
# =========================
|
| 22 |
+
# Config
|
| 23 |
+
# =========================
|
| 24 |
+
DEFAULT_PROMPT = (
|
| 25 |
+
"enhance microscopy image with subtle improvements, gently increase cellular boundary clarity, "
|
| 26 |
+
"preserve original morphological structure, maintain authentic texture patterns, "
|
| 27 |
+
"minimal noise reduction while keeping fine details intact"
|
| 28 |
+
)
|
| 29 |
+
|
| 30 |
+
GUIDANCE_SCALE = 2.0
|
| 31 |
+
NUM_INFERENCE_STEPS = 30
|
| 32 |
+
|
| 33 |
+
IMAGE_EXTENSIONS = {".jpg", ".jpeg", ".png", ".bmp", ".tiff", ".tif"}
|
| 34 |
+
|
| 35 |
+
MODEL_ID = "diffusers/FLUX.2-dev-bnb-4bit"
|
| 36 |
+
TORCH_DTYPE = torch.bfloat16
|
| 37 |
+
|
| 38 |
+
# =========================
|
| 39 |
+
# Global cached pipeline
|
| 40 |
+
# =========================
|
| 41 |
+
_pipe = None
|
| 42 |
+
|
| 43 |
+
|
| 44 |
+
def calculate_psnr_ssim(original: Image.Image, enhanced: Image.Image):
|
| 45 |
+
"""Calculate PSNR and SSIM between original and enhanced images."""
|
| 46 |
+
orig_float = img_as_float(np.array(original))
|
| 47 |
+
enh_float = img_as_float(np.array(enhanced))
|
| 48 |
+
|
| 49 |
+
# Ensure same shape (crop to min overlap)
|
| 50 |
+
if orig_float.shape != enh_float.shape:
|
| 51 |
+
min_h = min(orig_float.shape[0], enh_float.shape[0])
|
| 52 |
+
min_w = min(orig_float.shape[1], enh_float.shape[1])
|
| 53 |
+
orig_float = orig_float[:min_h, :min_w]
|
| 54 |
+
enh_float = enh_float[:min_h, :min_w]
|
| 55 |
+
|
| 56 |
+
psnr = peak_signal_noise_ratio(orig_float, enh_float, data_range=1.0)
|
| 57 |
+
|
| 58 |
+
if orig_float.ndim == 3:
|
| 59 |
+
ssim = structural_similarity(
|
| 60 |
+
orig_float, enh_float, data_range=1.0, channel_axis=-1
|
| 61 |
+
)
|
| 62 |
+
else:
|
| 63 |
+
ssim = structural_similarity(orig_float, enh_float, data_range=1.0)
|
| 64 |
+
|
| 65 |
+
return float(psnr), float(ssim)
|
| 66 |
+
|
| 67 |
+
|
| 68 |
+
def find_images(directory: str) -> List[str]:
|
| 69 |
+
"""Recursively find all images in a directory."""
|
| 70 |
+
image_files = []
|
| 71 |
+
for root, _, files in os.walk(directory):
|
| 72 |
+
for f in files:
|
| 73 |
+
if Path(f).suffix.lower() in IMAGE_EXTENSIONS:
|
| 74 |
+
image_files.append(os.path.join(root, f))
|
| 75 |
+
return image_files
|
| 76 |
+
|
| 77 |
+
|
| 78 |
+
def _get_pipe():
|
| 79 |
+
"""
|
| 80 |
+
Lazy-load the pipeline on local GPU.
|
| 81 |
+
"""
|
| 82 |
+
global _pipe
|
| 83 |
+
|
| 84 |
+
if _pipe is None:
|
| 85 |
+
if not torch.cuda.is_available():
|
| 86 |
+
raise RuntimeError(
|
| 87 |
+
"No GPU found. This tool requires a CUDA-compatible GPU to run."
|
| 88 |
+
)
|
| 89 |
+
|
| 90 |
+
print("Loading Flux model...")
|
| 91 |
+
_pipe = Flux2Pipeline.from_pretrained(
|
| 92 |
+
MODEL_ID,
|
| 93 |
+
torch_dtype=TORCH_DTYPE,
|
| 94 |
+
)
|
| 95 |
+
_pipe.to("cuda")
|
| 96 |
+
print(f"Model loaded successfully on GPU: {torch.cuda.get_device_name(0)}")
|
| 97 |
+
|
| 98 |
+
return _pipe
|
| 99 |
+
|
| 100 |
+
|
| 101 |
+
def process_images_cli(
|
| 102 |
+
input_paths: List[str],
|
| 103 |
+
output_dir: str,
|
| 104 |
+
prompt: str,
|
| 105 |
+
guidance_scale: float,
|
| 106 |
+
num_steps: int,
|
| 107 |
+
verbose: bool = True,
|
| 108 |
+
) -> Tuple[int, List[dict]]:
|
| 109 |
+
"""
|
| 110 |
+
Process images from input paths and save to output directory.
|
| 111 |
+
|
| 112 |
+
Args:
|
| 113 |
+
input_paths: List of file/directory paths (images or folders)
|
| 114 |
+
output_dir: Output directory for enhanced images
|
| 115 |
+
prompt: Enhancement prompt
|
| 116 |
+
guidance_scale: Guidance scale for inference
|
| 117 |
+
num_steps: Number of inference steps
|
| 118 |
+
verbose: Whether to print progress messages
|
| 119 |
+
|
| 120 |
+
Returns:
|
| 121 |
+
Tuple of (total_images_processed, results_list)
|
| 122 |
+
"""
|
| 123 |
+
if not input_paths:
|
| 124 |
+
raise ValueError("No input files provided")
|
| 125 |
+
|
| 126 |
+
if not prompt or prompt.strip() == "":
|
| 127 |
+
prompt = DEFAULT_PROMPT
|
| 128 |
+
|
| 129 |
+
# Create output directory
|
| 130 |
+
os.makedirs(output_dir, exist_ok=True)
|
| 131 |
+
|
| 132 |
+
try:
|
| 133 |
+
if verbose:
|
| 134 |
+
print("=" * 60)
|
| 135 |
+
print("Flux Microscopy Image Enhancement - CLI")
|
| 136 |
+
print("=" * 60)
|
| 137 |
+
print(f"Output directory: {output_dir}")
|
| 138 |
+
print(f"Prompt: {prompt}")
|
| 139 |
+
print(f"Guidance scale: {guidance_scale}")
|
| 140 |
+
print(f"Inference steps: {num_steps}")
|
| 141 |
+
print("=" * 60)
|
| 142 |
+
|
| 143 |
+
all_images = [] # list of tuples: (img_path, rel_path, base_dir_for_rel)
|
| 144 |
+
|
| 145 |
+
# Process each input path
|
| 146 |
+
for input_path in input_paths:
|
| 147 |
+
if not os.path.exists(input_path):
|
| 148 |
+
print(f"Warning: Path not found: {input_path}")
|
| 149 |
+
continue
|
| 150 |
+
|
| 151 |
+
# Check if it's a directory
|
| 152 |
+
if os.path.isdir(input_path):
|
| 153 |
+
if verbose:
|
| 154 |
+
print(f"\n[Scanning] Directory: {input_path} ...")
|
| 155 |
+
|
| 156 |
+
images = find_images(input_path)
|
| 157 |
+
for img_path in images:
|
| 158 |
+
rel_path = os.path.relpath(img_path, input_path)
|
| 159 |
+
all_images.append((img_path, rel_path, input_path))
|
| 160 |
+
|
| 161 |
+
if verbose:
|
| 162 |
+
print(f" Found {len(images)} images in directory")
|
| 163 |
+
|
| 164 |
+
# Check if it's an image file
|
| 165 |
+
elif os.path.isfile(input_path):
|
| 166 |
+
file_ext = Path(input_path).suffix.lower()
|
| 167 |
+
if file_ext in IMAGE_EXTENSIONS:
|
| 168 |
+
all_images.append((input_path, Path(input_path).name, None))
|
| 169 |
+
else:
|
| 170 |
+
print(f"Warning: Unsupported file format: {input_path}")
|
| 171 |
+
else:
|
| 172 |
+
print(f"Warning: Invalid path: {input_path}")
|
| 173 |
+
|
| 174 |
+
if not all_images:
|
| 175 |
+
raise ValueError("No valid images found in input files")
|
| 176 |
+
|
| 177 |
+
total_images = len(all_images)
|
| 178 |
+
if verbose:
|
| 179 |
+
print(f"\n[Processing] Total images to enhance: {total_images}")
|
| 180 |
+
print("-" * 60)
|
| 181 |
+
|
| 182 |
+
# Load pipeline
|
| 183 |
+
pipe = _get_pipe()
|
| 184 |
+
|
| 185 |
+
results = []
|
| 186 |
+
metrics_lines = []
|
| 187 |
+
|
| 188 |
+
for idx, (img_path, rel_path, base_dir) in enumerate(all_images, 1):
|
| 189 |
+
if verbose:
|
| 190 |
+
print(f"\n[{idx}/{total_images}] Processing: {Path(img_path).name}")
|
| 191 |
+
|
| 192 |
+
# Load input image
|
| 193 |
+
input_image = load_image(img_path)
|
| 194 |
+
|
| 195 |
+
# Run inference
|
| 196 |
+
enhanced_image = pipe(
|
| 197 |
+
image=input_image,
|
| 198 |
+
prompt=prompt,
|
| 199 |
+
guidance_scale=guidance_scale,
|
| 200 |
+
num_inference_steps=num_steps,
|
| 201 |
+
).images[0]
|
| 202 |
+
|
| 203 |
+
# Calculate metrics
|
| 204 |
+
psnr, ssim = calculate_psnr_ssim(input_image, enhanced_image)
|
| 205 |
+
|
| 206 |
+
if verbose:
|
| 207 |
+
print(f" PSNR: {psnr:.2f} dB | SSIM: {ssim:.4f}")
|
| 208 |
+
|
| 209 |
+
# Determine output path (preserve structure if from directory)
|
| 210 |
+
if base_dir:
|
| 211 |
+
output_rel_path = rel_path
|
| 212 |
+
else:
|
| 213 |
+
output_rel_path = rel_path
|
| 214 |
+
|
| 215 |
+
out_path = os.path.join(output_dir, output_rel_path)
|
| 216 |
+
os.makedirs(os.path.dirname(out_path), exist_ok=True)
|
| 217 |
+
|
| 218 |
+
# Add _flux suffix
|
| 219 |
+
out_name = Path(out_path).stem + "_flux" + Path(out_path).suffix
|
| 220 |
+
out_path = os.path.join(os.path.dirname(out_path), out_name)
|
| 221 |
+
|
| 222 |
+
# Save enhanced image
|
| 223 |
+
enhanced_image.save(out_path)
|
| 224 |
+
|
| 225 |
+
if verbose:
|
| 226 |
+
print(f" Saved to: {out_path}")
|
| 227 |
+
|
| 228 |
+
results.append(
|
| 229 |
+
{
|
| 230 |
+
"original_path": img_path,
|
| 231 |
+
"output_path": out_path,
|
| 232 |
+
"filename": output_rel_path,
|
| 233 |
+
"psnr": psnr,
|
| 234 |
+
"ssim": ssim,
|
| 235 |
+
}
|
| 236 |
+
)
|
| 237 |
+
|
| 238 |
+
metrics_lines.append(
|
| 239 |
+
f"{output_rel_path}: PSNR={psnr:.2f} dB, SSIM={ssim:.4f}"
|
| 240 |
+
)
|
| 241 |
+
|
| 242 |
+
# Print summary
|
| 243 |
+
if verbose:
|
| 244 |
+
avg_psnr = float(np.mean([r["psnr"] for r in results])) if results else 0.0
|
| 245 |
+
avg_ssim = float(np.mean([r["ssim"] for r in results])) if results else 0.0
|
| 246 |
+
|
| 247 |
+
print("\n" + "=" * 60)
|
| 248 |
+
print("SUMMARY")
|
| 249 |
+
print("=" * 60)
|
| 250 |
+
print(f"Total images processed: {total_images}")
|
| 251 |
+
print(f"Average PSNR: {avg_psnr:.2f} dB")
|
| 252 |
+
print(f"Average SSIM: {avg_ssim:.4f}")
|
| 253 |
+
print("\nIndividual metrics:")
|
| 254 |
+
for line in metrics_lines:
|
| 255 |
+
print(f" {line}")
|
| 256 |
+
print("=" * 60)
|
| 257 |
+
|
| 258 |
+
return total_images, results
|
| 259 |
+
|
| 260 |
+
except Exception as e:
|
| 261 |
+
print(f"\nError during processing: {str(e)}", file=sys.stderr)
|
| 262 |
+
raise
|
| 263 |
+
|
| 264 |
+
|
| 265 |
+
def main():
|
| 266 |
+
"""Main entry point for CLI."""
|
| 267 |
+
parser = argparse.ArgumentParser(
|
| 268 |
+
description="Flux Microscopy Image Enhancement - Command Line Interface",
|
| 269 |
+
formatter_class=argparse.RawDescriptionHelpFormatter,
|
| 270 |
+
epilog="""
|
| 271 |
+
Examples:
|
| 272 |
+
# Enhance a single image
|
| 273 |
+
python enhance_cli.py -i input.jpg -o output/
|
| 274 |
+
|
| 275 |
+
# Enhance multiple images with custom parameters
|
| 276 |
+
python enhance_cli.py -i image1.jpg image2.png -o output/ --guidance-scale 3.0 --steps 40
|
| 277 |
+
|
| 278 |
+
# Process all images in a directory
|
| 279 |
+
python enhance_cli.py -i images_folder/ -o output/
|
| 280 |
+
|
| 281 |
+
# Process with custom prompt
|
| 282 |
+
python enhance_cli.py -i input.jpg -o output/ --prompt "enhance cellular structure"
|
| 283 |
+
|
| 284 |
+
# Quiet mode (less verbose output)
|
| 285 |
+
python enhance_cli.py -i input.jpg -o output/ --quiet
|
| 286 |
+
|
| 287 |
+
Supported formats:
|
| 288 |
+
- Images: JPG, JPEG, PNG, BMP, TIFF, TIF
|
| 289 |
+
- Directories: Will recursively process all images inside
|
| 290 |
+
""",
|
| 291 |
+
)
|
| 292 |
+
|
| 293 |
+
# Required arguments
|
| 294 |
+
parser.add_argument(
|
| 295 |
+
"-i",
|
| 296 |
+
"--input",
|
| 297 |
+
nargs="+",
|
| 298 |
+
required=True,
|
| 299 |
+
help="Input path(s) - image files or directories. Multiple paths supported.",
|
| 300 |
+
)
|
| 301 |
+
|
| 302 |
+
parser.add_argument(
|
| 303 |
+
"-o", "--output", required=True, help="Output directory for enhanced images"
|
| 304 |
+
)
|
| 305 |
+
|
| 306 |
+
# Optional arguments
|
| 307 |
+
parser.add_argument(
|
| 308 |
+
"-p",
|
| 309 |
+
"--prompt",
|
| 310 |
+
default=DEFAULT_PROMPT,
|
| 311 |
+
help=f"Enhancement prompt (default: '{DEFAULT_PROMPT[:50]}...')",
|
| 312 |
+
)
|
| 313 |
+
|
| 314 |
+
parser.add_argument(
|
| 315 |
+
"-g",
|
| 316 |
+
"--guidance-scale",
|
| 317 |
+
type=float,
|
| 318 |
+
default=GUIDANCE_SCALE,
|
| 319 |
+
help=f"Guidance scale (1.0-5.0, lower=conservative, higher=creative, default: {GUIDANCE_SCALE})",
|
| 320 |
+
)
|
| 321 |
+
|
| 322 |
+
parser.add_argument(
|
| 323 |
+
"-s",
|
| 324 |
+
"--steps",
|
| 325 |
+
type=int,
|
| 326 |
+
default=NUM_INFERENCE_STEPS,
|
| 327 |
+
help=f"Number of inference steps (10-50, more=better quality but slower, default: {NUM_INFERENCE_STEPS})",
|
| 328 |
+
)
|
| 329 |
+
|
| 330 |
+
parser.add_argument(
|
| 331 |
+
"-q",
|
| 332 |
+
"--quiet",
|
| 333 |
+
action="store_true",
|
| 334 |
+
help="Quiet mode - reduce output verbosity",
|
| 335 |
+
)
|
| 336 |
+
|
| 337 |
+
args = parser.parse_args()
|
| 338 |
+
|
| 339 |
+
# Validate arguments
|
| 340 |
+
if args.guidance_scale < 1.0 or args.guidance_scale > 5.0:
|
| 341 |
+
parser.error("guidance-scale must be between 1.0 and 5.0")
|
| 342 |
+
|
| 343 |
+
if args.steps < 10 or args.steps > 50:
|
| 344 |
+
parser.error("steps must be between 10 and 50")
|
| 345 |
+
|
| 346 |
+
# Process images
|
| 347 |
+
try:
|
| 348 |
+
total, results = process_images_cli(
|
| 349 |
+
input_paths=args.input,
|
| 350 |
+
output_dir=args.output,
|
| 351 |
+
prompt=args.prompt,
|
| 352 |
+
guidance_scale=args.guidance_scale,
|
| 353 |
+
num_steps=args.steps,
|
| 354 |
+
verbose=not args.quiet,
|
| 355 |
+
)
|
| 356 |
+
|
| 357 |
+
if not args.quiet:
|
| 358 |
+
print("\n✅ Enhancement completed successfully!")
|
| 359 |
+
print(f"📁 Output directory: {args.output}")
|
| 360 |
+
|
| 361 |
+
sys.exit(0)
|
| 362 |
+
|
| 363 |
+
except Exception as e:
|
| 364 |
+
print(f"\n❌ Error: {str(e)}", file=sys.stderr)
|
| 365 |
+
sys.exit(1)
|
| 366 |
+
|
| 367 |
+
|
| 368 |
+
if __name__ == "__main__":
|
| 369 |
+
main()
|