import cv2 import numpy as np import math import torch import random from PIL import Image from torch.utils.data import DataLoader from torchvision.transforms import Resize torch.manual_seed(12345) random.seed(12345) np.random.seed(12345) device = torch.device("cuda") if torch.cuda.is_available() else torch.device("cpu") class WireframeExtractor: def __call__(self, image: np.ndarray): """ Extract corners of wireframe from a barnacle image :param image: Numpy RGB image of shape (W, H, 3) :return [x1, y1, x2, y2] """ h, w = image.shape[:2] imghsv = cv2.cvtColor(image, cv2.COLOR_RGB2HSV) hsvblur = cv2.GaussianBlur(imghsv, (9, 9), 0) lower = np.array([70, 20, 20]) upper = np.array([130, 255, 255]) color_mask = cv2.inRange(hsvblur, lower, upper) invert = cv2.bitwise_not(color_mask) contours, _ = cv2.findContours(invert, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE) max_contour = contours[0] largest_area = 0 for index, contour in enumerate(contours): area = cv2.contourArea(contour) if area > largest_area: if cv2.pointPolygonTest(contour, (w / 2, h / 2), False) == 1: largest_area = area max_contour = contour x, y, w, h = cv2.boundingRect(max_contour) # return [x, y, x + w, y + h] return x,y,w,h wireframe_extractor = WireframeExtractor() def show_anns(anns): if len(anns) == 0: return sorted_anns = sorted(anns, key=(lambda x: x['area']), reverse=True) ax = plt.gca() ax.set_autoscale_on(False) polygons = [] color = [] for ann in sorted_anns: m = ann['segmentation'] img = np.ones((m.shape[0], m.shape[1], 3)) color_mask = np.random.random((1, 3)).tolist()[0] for i in range(3): img[:,:,i] = color_mask[i] ax.imshow(np.dstack((img, m*0.35))) from segment_anything import sam_model_registry, SamAutomaticMaskGenerator, SamPredictor model = sam_model_registry["default"](checkpoint="./sam_vit_h_4b8939.pth") model.to(device) predictor = SamPredictor(model) mask_generator = SamAutomaticMaskGenerator(model) import gradio as gr import matplotlib.pyplot as plt import io def check_circularity(segmentation): img_u8 = segmentation.astype(np.uint8) im_gauss = cv2.GaussianBlur(img_u8, (5, 5), 0) ret, thresh = cv2.threshold(im_gauss, 0, 255, cv2.THRESH_BINARY) contours, hierarchy = cv2.findContours(thresh, cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE) con = contours[0] perimeter = cv2.arcLength(con, True) area = cv2.contourArea(con) if perimeter != 0: circularity = 4*math.pi*(area/(perimeter*perimeter)) if 0.8 < circularity < 1.2: return True else: return circularity def count_barnacles(image_raw, split_num, progress=gr.Progress()): progress(0, desc="Finding bounding wire") corners = wireframe_extractor(image_raw) print(corners) # (0, 0, 1254, 1152) cropped_image = image_raw[corners[1]:corners[3]+corners[1], corners[0]:corners[2]+corners[0], :] print(cropped_image.shape) split_num = 5 x_inc = int(cropped_image.shape[0]/split_num) y_inc = int(cropped_image.shape[1]/split_num) startx = -x_inc mask_counter = 0 good_masks = [] centers = [] for r in range(0, split_num): startx += x_inc starty = -y_inc for c in range(0, split_num): starty += y_inc small_image = cropped_image[starty:starty+y_inc, startx:startx+x_inc, :] # plt.figure() # plt.imshow(small_image) # plt.axis('on') progress(0, desc=f"Encoding crop {r*split_num + c}/{split_num ** 2}") mask_generator.predictor.set_image(small_image) progress(0, desc=f"Generating masks for crop {r*split_num + c}/{split_num ** 2}") masks = mask_generator.generate(small_image) num_masks = len(masks) for idx, mask in enumerate(masks): progress(float(idx)/float(num_masks), desc=f"Processing masks for crop {r*split_num + c}/{split_num ** 2}") circular = check_circularity(mask['segmentation']) if circular and mask['area']>500 and mask['area'] < 10000: mask_counter += 1 good_masks.append(mask) box = mask['bbox'] centers.append((box[0] + box[2]/2 + corners[0] + startx, box[1] + box[3]/2 + corners[1] + starty)) progress(0, desc="Generating Plot") # Create a figure with a size of 10 inches by 10 inches fig = plt.figure(figsize=(10, 10)) # Display the image using the imshow() function # plt.imshow(cropped_image) plt.imshow(image_raw) # Call the custom function show_anns() to plot annotations on top of the image # show_anns(good_masks) for coord in centers: plt.scatter(coord[0], coord[1], marker="x", color="red", s=32) # Turn off the axis plt.axis('off') # Get the plot as a numpy array # buf = io.BytesIO() # plt.savefig(buf, format='png', bbox_inches='tight', pad_inches=0) # buf.seek(0) # img_arr = np.frombuffer(buf.getvalue(), dtype=np.uint8) # buf.close() # # Decode the numpy array to an image # annotated = cv2.imdecode(img_arr, 1) # annotated = cv2.cvtColor(annotated, cv2.COLOR_BGR2RGB) # # Close the figure # plt.close(fig) # return annotated, mask_counter, centers return fig, mask_counter, centers demo = gr.Interface(count_barnacles, inputs=[ gr.Image(type="numpy", label="Input Image"), ], outputs=[ # gr.Image(type="numpy", label="Annotated Image"), gr.Plot(label="Annotated Image"), gr.Number(label="Predicted Number of Barnacles"), gr.Dataframe(type="array", headers=["x", "y"], label="Mask centers") # gr.Number(label="Actual Number of Barnacles"), # gr.Number(label="Custom Metric") ]) # examples="examples") demo.queue(concurrency_count=10).launch()