app.py

from segment_anything import sam_model_registry, SamPredictor
import torch
import cv2
import numpy as np
import gradio as gr
import pandas as pd
import matplotlib.pyplot as plt

# Load SAM model
sam_checkpoint = "sam_vit_h.pth"  # Checkpoint file (download it from Meta AI)
device = "cuda" if torch.cuda.is_available() else "cpu"
model_type = "vit_h"
sam = sam_model_registry[model_type](checkpoint=sam_checkpoint).to(device)
predictor = SamPredictor(sam)

def preprocess_image(image):
    """Convert image to RGB format for SAM."""
    if len(image.shape) == 2:
        image = cv2.cvtColor(image, cv2.COLOR_GRAY2RGB)
    return image

def detect_blood_cells(image):
    """Detect blood cells using SAM."""
    image = preprocess_image(image)
    predictor.set_image(image)

    # Generate automatic masks (SAM can also take prompts for guided segmentation)
    masks, _, _ = predictor.predict(
        point_coords=None, 
        point_labels=None, 
        multimask_output=True
    )

    contours_list = []
    features = []
    for i, mask in enumerate(masks):
        mask = mask.astype(np.uint8) * 255  # Convert boolean mask to uint8
        contours, _ = cv2.findContours(mask, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)

        for j, contour in enumerate(contours, 1):
            area = cv2.contourArea(contour)
            perimeter = cv2.arcLength(contour, True)
            circularity = 4 * np.pi * area / (perimeter * perimeter) if perimeter > 0 else 0

            if 100 < area < 5000 and circularity > 0.7:
                M = cv2.moments(contour)
                if M["m00"] != 0:
                    cx = int(M["m10"] / M["m00"])
                    cy = int(M["m01"] / M["m00"])
                    features.append({
                        'label': f"{i}-{j}", 'area': area, 'perimeter': perimeter,
                        'circularity': circularity, 'centroid_x': cx, 'centroid_y': cy
                    })
                contours_list.append(contour)

    return contours_list, features, masks

def process_image(image):
    if image is None:
        return None, None, None, None

    contours, features, masks = detect_blood_cells(image)
    vis_img = image.copy()

    for feature in features:
        contour = contours[int(feature['label'].split('-')[1]) - 1]
        cv2.drawContours(vis_img, [contour], -1, (0, 255, 0), 2)
        cv2.putText(vis_img, str(feature['label']), (feature['centroid_x'], feature['centroid_y']),
                    cv2.FONT_HERSHEY_SIMPLEX, 0.5, (0, 0, 255), 1)

    df = pd.DataFrame(features)
    return vis_img, masks[0], df

def analyze(image):
    vis_img, mask, df = process_image(image)

    plt.style.use('dark_background')
    fig, axes = plt.subplots(1, 2, figsize=(12, 5))

    if not df.empty:
        axes[0].hist(df['area'], bins=20, color='cyan', edgecolor='black')
        axes[0].set_title('Cell Size Distribution')

        axes[1].scatter(df['area'], df['circularity'], alpha=0.6, c='magenta')
        axes[1].set_title('Area vs Circularity')

    return vis_img, mask, fig, df

# Gradio Interface
demo = gr.Interface(fn=analyze, inputs=gr.Image(type="numpy"), outputs=[gr.Image(), gr.Image(), gr.Plot(), gr.Dataframe()])
demo.launch()