app.py

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

# Ensure the SAM model checkpoint is downloaded
SAM_CHECKPOINT = "sam_vit_h.pth"  # Update path if needed
MODEL_TYPE = "vit_h"

# Check if CUDA is available for GPU processing
DEVICE = "cuda" if torch.cuda.is_available() else "cpu"

# Load the SAM model
try:
    sam = sam_model_registry[MODEL_TYPE](checkpoint=SAM_CHECKPOINT).to(DEVICE)
    mask_generator = SamAutomaticMaskGenerator(sam)
except FileNotFoundError:
    raise FileNotFoundError(f"Checkpoint file '{SAM_CHECKPOINT}' not found. Download it from: https://github.com/facebookresearch/segment-anything")

def preprocess_image(image):
    """Convert image to grayscale and apply adaptive thresholding for better cell detection."""
    if len(image.shape) == 2:
        image = cv2.cvtColor(image, cv2.COLOR_GRAY2RGB)

    gray = cv2.cvtColor(image, cv2.COLOR_RGB2GRAY)

    # Apply adaptive thresholding for better contrast
    adaptive_thresh = cv2.adaptiveThreshold(
        gray, 255, cv2.ADAPTIVE_THRESH_GAUSSIAN_C, cv2.THRESH_BINARY_INV, 11, 2
    )

    # Morphological operations to remove noise
    kernel = np.ones((3, 3), np.uint8)
    clean_mask = cv2.morphologyEx(adaptive_thresh, cv2.MORPH_CLOSE, kernel, iterations=2)
    clean_mask = cv2.morphologyEx(clean_mask, cv2.MORPH_OPEN, kernel, iterations=2)

    return clean_mask

def detect_blood_cells(image):
    """Detect blood cells using SAM segmentation + contour analysis."""
    # Generate masks using SAM
    masks = mask_generator.generate(image)

    features = []
    processed_image = image.copy()

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

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

            # Filter small or irregular shapes
            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": len(features) + 1,
                            "area": area,
                            "perimeter": perimeter,
                            "circularity": circularity,
                            "centroid_x": cx,
                            "centroid_y": cy,
                        }
                    )

                    # Draw detected cell on image
                    cv2.drawContours(processed_image, [contour], -1, (0, 255, 0), 2)
                    cv2.putText(
                        processed_image,
                        str(len(features)),
                        (cx, cy),
                        cv2.FONT_HERSHEY_SIMPLEX,
                        0.5,
                        (0, 0, 255),
                        1,
                    )

    return processed_image, features

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

    processed_img, features = detect_blood_cells(image)
    df = pd.DataFrame(features)

    return processed_img, df

def analyze(image):
    processed_img, 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 processed_img, fig, df

# Gradio Interface
demo = gr.Interface(
    fn=analyze,
    inputs=gr.Image(type="numpy"),
    outputs=[gr.Image(), gr.Plot(), gr.Dataframe()],
    title="Blood Cell Detection",
    description="Detect and analyze blood cells using SAM segmentation & contour analysis.",
)

demo.launch()