import argparse import os import torch import numpy as np import skimage import skimage.measure import skimage.io import shapely.geometry import shapely.ops from PIL import Image from multiprocess import Pool from tqdm import tqdm from functools import partial from lydorn_utils import print_utils, geo_utils from frame_field_learning import polygonize_utils, plot_utils DEBUG = False def debug_print(s: str): if DEBUG: print_utils.print_debug(s) def get_args(): argparser = argparse.ArgumentParser(description=__doc__) argparser.add_argument( '--seg_filepath', required=True, nargs='*', type=str, help='Filepath(s) to input segmentation/mask image.') argparser.add_argument( '--im_dirpath', required=True, type=str, help='Path to the directory containing the corresponding images os the segmentation/mask. ' 'Files must have the same filename as --seg_filepath.' 'Used for vizualization or saving the shapefile with the same coordinate system as that image.') argparser.add_argument( '--out_dirpath', required=True, type=str, help='Path to the output directory.') argparser.add_argument( '--out_ext', type=str, default="shp", choices=['pdf', 'shp'], help="File extension of the output. " "'pdf': pdf visualization (requires --im_dirpath for the image), 'shp': shapefile") argparser.add_argument( '--bbox', nargs='*', type=int, help='Selects area in bbox for computation.') args = argparser.parse_args() return args def simplify(polygons, probs, tolerance): if type(tolerance) == list: out_polygons_dict = {} out_probs_dict = {} for tol in tolerance: out_polygons, out_probs = simplify(polygons, probs, tol) out_polygons_dict["tol_{}".format(tol)] = out_polygons out_probs_dict["tol_{}".format(tol)] = out_probs return out_polygons_dict, out_probs_dict else: out_polygons = [polygon.simplify(tolerance, preserve_topology=True) for polygon in polygons] return out_polygons, probs def shapely_postprocess(out_contours, np_indicator, config): height = np_indicator.shape[0] width = np_indicator.shape[1] # Handle holes: line_string_list = [shapely.geometry.LineString(out_contour[:, ::-1]) for out_contour in out_contours] # Add image boundary line_strings for border polygons line_string_list.append( shapely.geometry.LinearRing([ (0, 0), (0, height - 1), (width - 1, height - 1), (width - 1, 0), ])) # Merge polylines (for border polygons): multi_line_string = shapely.ops.unary_union(line_string_list) # Find polygons: polygons, dangles, cuts, invalids = shapely.ops.polygonize_full(multi_line_string) polygons = list(polygons) # Remove small polygons polygons = [polygon for polygon in polygons if config["min_area"] < polygon.area] # Remove low prob polygons filtered_polygons = [] filtered_polygon_probs = [] for polygon in polygons: prob = polygonize_utils.compute_geom_prob(polygon, np_indicator) # print("simple:", np_indicator.min(), np_indicator.mean(), np_indicator.max(), prob) if config["seg_threshold"] < prob: filtered_polygons.append(polygon) filtered_polygon_probs.append(prob) polygons, probs = simplify(filtered_polygons, filtered_polygon_probs, config["tolerance"]) return polygons, probs def polygonize(seg_batch, config, pool=None, pre_computed=None): # tic_total = time.time() assert len(seg_batch.shape) == 4 and seg_batch.shape[ 1] <= 3, "seg_batch should be (N, C, H, W) with C <= 3, not {}".format(seg_batch.shape) # Indicator # tic = time.time() indicator_batch = seg_batch[:, 0, :, :] np_indicator_batch = indicator_batch.cpu().numpy() # toc = time.time() # debug_print(f"Indicator to cpu: {toc - tic}s") if pre_computed is None or "init_contours_batch" not in pre_computed: # tic = time.time() init_contours_batch = polygonize_utils.compute_init_contours_batch(np_indicator_batch, config["data_level"], pool=pool) # toc = time.time() # debug_print(f"Init contours: {toc - tic}s") else: init_contours_batch = pre_computed["init_contours_batch"] # tic = time.time() # Convert contours to shapely polygons to handle holes: if pool is not None: shapely_postprocess_partial = partial(shapely_postprocess, config=config) polygons_probs_batch = pool.starmap(shapely_postprocess_partial, zip(init_contours_batch, np_indicator_batch)) polygons_batch, probs_batch = zip(*polygons_probs_batch) else: polygons_batch = [] probs_batch = [] for i, out_contours in enumerate(init_contours_batch): polygons, probs = shapely_postprocess(out_contours, np_indicator_batch[i], config) polygons_batch.append(polygons) probs_batch.append(probs) # toc = time.time() # debug_print(f"Shapely post-process: {toc - tic}s") # toc_total = time.time() # debug_print(f"Total: {toc_total - tic_total}s") return polygons_batch, probs_batch def run_one(seg_filepath, out_dirpath, config, im_dirpath, out_ext=None, bbox=None): filename = os.path.basename(seg_filepath) name = os.path.splitext(filename)[0] # Load image image = None im_filepath = os.path.join(im_dirpath, name + ".tif") if out_ext == "pdf": image = skimage.io.imread(im_filepath) # seg = skimage.io.imread(seg_filepath) / 255 seg_img = Image.open(seg_filepath) seg = np.array(seg_img) if seg.dtype == np.uint8: seg = seg / 255 elif seg.dtype == np.bool: seg = seg.astype(np.float) # Select bbox for dev if bbox is not None: assert len(bbox) == 4, "bbox should have 4 values" # bbox = [1440, 210, 1800, 650] # vienna12 # bbox = [2808, 2393, 3124, 2772] # innsbruck19 if image is not None: image = image[bbox[0]:bbox[2], bbox[1]:bbox[3]] seg = seg[bbox[0]:bbox[2], bbox[1]:bbox[3]] extra_name = ".bbox_{}_{}_{}_{}".format(*bbox) else: extra_name = "" # Convert to torch and add batch dim if len(seg.shape) < 3: seg = seg[:, :, None] seg_batch = torch.tensor(np.transpose(seg[:, :, :2], (2, 0, 1)), dtype=torch.float)[None, ...] out_contours_batch, out_probs_batch = polygonize(seg_batch, config) polygons = out_contours_batch[0] if out_ext == "shp": out_filepath = os.path.join(out_dirpath, name + ".shp") geo_utils.save_shapefile_from_shapely_polygons(polygons, im_filepath, out_filepath) elif out_ext == "pdf": base_filepath = os.path.splitext(seg_filepath)[0] filepath = base_filepath + extra_name + ".poly_simple.pdf" # plot_utils.save_poly_viz(image, polygons, filepath, linewidths=1, draw_vertices=True, color_choices=[[0, 1, 0, 1]]) plot_utils.save_poly_viz(image, polygons, filepath, markersize=30, linewidths=1, draw_vertices=True) else: raise ValueError(f"out_ext should be shp or pdf, not {out_ext}") def main(): config = { "data_level": 0.5, "tolerance": 1.0, "seg_threshold": 0.5, "min_area": 10 } # --- Process args --- # args = get_args() pool = Pool() list(tqdm(pool.imap(partial(run_one, out_dirpath=args.out_dirpath, config=config, im_dirpath=args.im_dirpath, out_ext=args.out_ext, bbox=args.bbox), args.seg_filepath), desc="Simple poly.", total=len(args.seg_filepath))) if __name__ == '__main__': main()