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plotIceConcentration.py
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import argparse, os, sys
import numpy as np
import pandas as pd
from skimage.io import imread, imsave
from matplotlib import pyplot as plt
import cv2
import time
from pprint import pprint, pformat
from tabulate import tabulate
from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas
from matplotlib.figure import Figure
# plt.style.use('presentation')
import densenet.evaluation.eval_segm as eval
from densenet.utils import read_data, getDateTime, print_and_write, resize_ar, put_text_with_background, col_bgr
from dictances import bhattacharyya, euclidean, mae, mse
def getPlotImage(data_x, data_y, cols, title, line_labels, x_label, y_label, ylim=None, legend=1):
cols = [(col[0] / 255.0, col[1] / 255.0, col[2] / 255.0) for col in cols]
fig = Figure(
# figsize=(6.4, 3.6), dpi=300,
figsize=(4.8, 2.7), dpi=400,
# edgecolor='k',
# facecolor ='k'
)
# fig.tight_layout()
# fig.set_tight_layout(True)
fig.subplots_adjust(
bottom=0.17,
right=0.95,
)
canvas = FigureCanvas(fig)
ax = fig.gca()
n_data = len(data_y)
for i in range(n_data):
datum_y = data_y[i]
line_label = line_labels[i]
col = cols[i]
args = {
'color': col
}
if legend:
args['label'] = line_label
ax.plot(data_x, datum_y, **args)
plt.rcParams['axes.titlesize'] = 10
# fontdict = {'fontsize': plt.rcParams['axes.titlesize'],
# 'fontweight': plt.rcParams['axes.titleweight'],
# 'verticalalignment': 'baseline',
# 'horizontalalignment': plt.loc
# }
ax.set_title(title,
# fontdict=fontdict
)
if legend:
ax.legend(fancybox=True, framealpha=0.1)
ax.grid(1)
ax.set_xlabel(x_label)
ax.set_ylabel(y_label)
if ylim is not None:
ax.set_ylim(*ylim)
canvas.draw()
width, height = fig.get_size_inches() * fig.get_dpi()
plot_img = np.fromstring(canvas.tostring_rgb(), dtype='uint8').reshape(
int(height), int(width), 3)
return plot_img
def str_to_list(_str, _type=str, _sep=','):
if _sep not in _str:
_str += _sep
return [k for k in list(map(_type, _str.split(_sep))) if k]
def main():
parser = argparse.ArgumentParser()
parser.add_argument("--log_dir", type=str)
parser.add_argument("--images_path", type=str)
parser.add_argument("--images_ext", type=str, default='png')
parser.add_argument("--labels_path", type=str, default='')
parser.add_argument("--labels_ext", type=str, default='png')
parser.add_argument("--labels_col", type=str, default='green')
parser.add_argument("--seg_paths", type=str_to_list, default=[])
parser.add_argument("--seg_ext", type=str, default='png')
parser.add_argument("--seg_root_dir", type=str, default='')
parser.add_argument("--seg_labels", type=str_to_list, default=[])
parser.add_argument("--seg_cols", type=str_to_list, default=['blue', 'forest_green', 'magenta', 'cyan', 'red'])
parser.add_argument("--out_path", type=str, default='')
parser.add_argument("--out_ext", type=str, default='jpg')
parser.add_argument("--out_size", type=str, default='1920x1080')
parser.add_argument("--fps", type=float, default=30)
parser.add_argument("--codec", type=str, default='H264')
parser.add_argument("--save_path", type=str, default='')
parser.add_argument("--n_classes", type=int)
parser.add_argument("--save_stitched", type=int, default=0)
parser.add_argument("--load_ice_conc_diff", type=int, default=0)
parser.add_argument("--start_id", type=int, default=0)
parser.add_argument("--end_id", type=int, default=-1)
parser.add_argument("--show_img", type=int, default=0)
parser.add_argument("--stitch", type=int, default=0)
parser.add_argument("--stitch_seg", type=int, default=1)
parser.add_argument("--plot_changed_seg_count", type=int, default=0)
parser.add_argument("--normalize_labels", type=int, default=0)
parser.add_argument("--selective_mode", type=int, default=0)
parser.add_argument("--ice_type", type=int, default=0, help='0: combined, 1: anchor, 2: frazil')
parser.add_argument("--enable_plotting", type=int, default=1, help='enable_plotting')
args = parser.parse_args()
images_path = args.images_path
images_ext = args.images_ext
labels_path = args.labels_path
labels_ext = args.labels_ext
labels_col = args.labels_col
seg_paths = args.seg_paths
seg_root_dir = args.seg_root_dir
seg_ext = args.seg_ext
out_path = args.out_path
out_ext = args.out_ext
out_size = args.out_size
fps = args.fps
codec = args.codec
# save_path = args.save_path
n_classes = args.n_classes
end_id = args.end_id
start_id = args.start_id
show_img = args.show_img
stitch = args.stitch
stitch_seg = args.stitch_seg
save_stitched = args.save_stitched
normalize_labels = args.normalize_labels
selective_mode = args.selective_mode
seg_labels = args.seg_labels
seg_cols = args.seg_cols
ice_type = args.ice_type
plot_changed_seg_count = args.plot_changed_seg_count
load_ice_conc_diff = args.load_ice_conc_diff
enable_plotting = args.enable_plotting
ice_types = {
0: 'Ice',
1: 'Anchor Ice',
2: 'Frazil Ice',
}
loc = (5, 120)
size = 8
thickness = 6
fgr_col = (255, 255, 255)
bgr_col = (0, 0, 0)
font_id = 0
video_exts = ['mp4', 'mkv', 'avi', 'mpg', 'mpeg', 'mjpg']
labels_col_rgb = col_bgr[labels_col]
seg_cols_rgb = [col_bgr[seg_col] for seg_col in seg_cols]
ice_type_str = ice_types[ice_type]
print('ice_type_str: {}'.format(ice_type_str))
src_files, src_labels_list, total_frames = read_data(images_path, images_ext, labels_path,
labels_ext)
if end_id < start_id:
end_id = total_frames - 1
if seg_paths:
n_seg_paths = len(seg_paths)
n_seg_labels = len(seg_labels)
if n_seg_paths != n_seg_labels:
raise IOError('Mismatch between n_seg_labels: {} and n_seg_paths: {}'.format(
n_seg_labels, n_seg_paths
))
if seg_root_dir:
seg_paths = [os.path.join(seg_root_dir, name) for name in seg_paths]
if not out_path:
if labels_path:
out_path = labels_path + '_conc'
elif seg_paths:
out_path = seg_paths[0] + '_conc'
if not os.path.isdir(out_path):
os.makedirs(out_path)
# print('Saving results data to {}'.format(out_path))
# if not save_path:
# save_path = os.path.join(os.path.dirname(images_path), 'ice_concentration')
# if not os.path.isdir(save_path):
# os.makedirs(save_path)
# if stitch and save_stitched:
# print('Saving ice_concentration plots to: {}'.format(save_path))
# log_fname = os.path.join(out_path, 'vis_log_{:s}.txt'.format(getDateTime()))
# print('Saving log to: {}'.format(log_fname))
if selective_mode:
label_diff = int(255.0 / n_classes)
else:
label_diff = int(255.0 / (n_classes - 1))
print('label_diff: {}'.format(label_diff))
n_frames = end_id - start_id + 1
print_diff = int(n_frames * 0.01)
labels_img = None
n_cols = len(seg_cols_rgb)
plot_y_label = '{} concentration (%)'.format(ice_type_str)
plot_x_label = 'distance in pixels from left edge'
dists = {}
for _label in seg_labels:
dists[_label] = {
# 'bhattacharyya': [],
'euclidean': [],
'mae': [],
'mse': [],
# 'frobenius': [],
}
plot_title = '{} concentration'.format(ice_type_str)
out_size = tuple([int(x) for x in out_size.split('x')])
write_to_video = out_ext in video_exts
out_width, out_height = out_size
out_seq_name = os.path.basename(out_path)
if enable_plotting:
if write_to_video:
stitched_seq_path = os.path.join(out_path, '{}.{}'.format(out_seq_name, out_ext))
print('Writing {}x{} output video to: {}'.format(out_width, out_height, stitched_seq_path))
save_dir = os.path.dirname(stitched_seq_path)
fourcc = cv2.VideoWriter_fourcc(*codec)
video_out = cv2.VideoWriter(stitched_seq_path, fourcc, fps, out_size)
else:
stitched_seq_path = os.path.join(out_path, out_seq_name)
print('Writing {}x{} output images of type {} to: {}'.format(
out_width, out_height, out_ext, stitched_seq_path))
save_dir = stitched_seq_path
if save_dir and not os.path.isdir(save_dir):
os.makedirs(save_dir)
prev_seg_img = {}
prev_conc_data_y = {}
changed_seg_count = {}
ice_concentration_diff = {}
if load_ice_conc_diff:
for seg_id in seg_labels:
ice_concentration_diff[seg_id] = np.loadtxt(
os.path.join(out_path, '{}_ice_concentration_diff.txt'.format(seg_id)),
dtype=np.float64)
_pause = 0
mae_data_y = []
for seg_id, _ in enumerate(seg_paths):
mae_data_y.append([])
for img_id in range(start_id, end_id + 1):
start_t = time.time()
# img_fname = '{:s}_{:d}.{:s}'.format(fname_templ, img_id + 1, img_ext)
img_fname = src_files[img_id]
img_fname_no_ext = os.path.splitext(img_fname)[0]
src_img_fname = os.path.join(images_path, img_fname)
src_img = imread(src_img_fname)
if src_img is None:
raise SystemError('Source image could not be read from: {}'.format(src_img_fname))
try:
src_height, src_width = src_img.shape[:2]
except ValueError as e:
print('src_img_fname: {}'.format(src_img_fname))
print('src_img: {}'.format(src_img))
print('src_img.shape: {}'.format(src_img.shape))
print('error: {}'.format(e))
sys.exit(1)
conc_data_x = np.asarray(range(src_width), dtype=np.float64)
plot_data_x = conc_data_x
plot_data_y = []
plot_cols = []
plot_labels = []
stitched_img = src_img
if labels_path:
labels_img_fname = os.path.join(labels_path, img_fname_no_ext + '.{}'.format(labels_ext))
labels_img_orig = imread(labels_img_fname)
if labels_img_orig is None:
raise SystemError('Labels image could not be read from: {}'.format(labels_img_fname))
labels_height, labels_width = labels_img_orig.shape[:2]
if labels_height != src_height or labels_width != src_width:
raise AssertionError('Mismatch between dimensions of source: {} and label: {}'.format(
(src_height, src_width), (seg_height, seg_width)
))
if len(labels_img_orig.shape) == 3:
labels_img_orig = np.squeeze(labels_img_orig[:, :, 0])
if show_img:
cv2.imshow('labels_img_orig', labels_img_orig)
if normalize_labels:
labels_img = (labels_img_orig.astype(np.float64) / label_diff).astype(np.uint8)
else:
labels_img = np.copy(labels_img_orig)
if len(labels_img.shape) == 3:
labels_img = labels_img[:, :, 0].squeeze()
conc_data_y = np.zeros((labels_width,), dtype=np.float64)
for i in range(labels_width):
curr_pix = np.squeeze(labels_img[:, i])
if ice_type == 0:
ice_pix = curr_pix[curr_pix != 0]
else:
ice_pix = curr_pix[curr_pix == ice_type]
conc_data_y[i] = (len(ice_pix) / float(src_height)) * 100.0
conc_data = np.zeros((labels_width, 2), dtype=np.float64)
conc_data[:, 0] = conc_data_x
conc_data[:, 1] = conc_data_y
plot_data_y.append(conc_data_y)
plot_cols.append(labels_col_rgb)
gt_dict = {conc_data_x[i]: conc_data_y[i] for i in range(labels_width)}
if not normalize_labels:
labels_img_orig = (labels_img_orig.astype(np.float64) * label_diff).astype(np.uint8)
if len(labels_img_orig.shape) == 2:
labels_img_orig = np.stack((labels_img_orig, labels_img_orig, labels_img_orig), axis=2)
stitched_img = np.concatenate((stitched_img, labels_img_orig), axis=1)
plot_labels.append('GT')
# gt_cl, _ = eval.extract_classes(labels_img_orig)
# print('gt_cl: {}'.format(gt_cl))
mean_seg_counts = {}
seg_count_data_y = []
curr_mae_data_y = []
mean_conc_diff = {}
conc_diff_data_y = []
seg_img_disp_list = []
for seg_id, seg_path in enumerate(seg_paths):
seg_img_fname = os.path.join(seg_path, img_fname_no_ext + '.{}'.format(seg_ext))
seg_img_orig = imread(seg_img_fname)
seg_col = seg_cols_rgb[seg_id % n_cols]
_label = seg_labels[seg_id]
if seg_img_orig is None:
raise SystemError('Seg image could not be read from: {}'.format(seg_img_fname))
seg_height, seg_width = seg_img_orig.shape[:2]
if seg_height != src_height or seg_width != src_width:
raise AssertionError('Mismatch between dimensions of source: {} and seg: {}'.format(
(src_height, src_width), (seg_height, seg_width)
))
if len(seg_img_orig.shape) == 3:
seg_img_orig = np.squeeze(seg_img_orig[:, :, 0])
if seg_img_orig.max() > n_classes - 1:
seg_img = (seg_img_orig.astype(np.float64) / label_diff).astype(np.uint8)
seg_img_disp = seg_img_orig
else:
seg_img = seg_img_orig
seg_img_disp = (seg_img_orig.astype(np.float64) * label_diff).astype(np.uint8)
if len(seg_img_disp.shape) == 2:
seg_img_disp = np.stack((seg_img_disp, seg_img_disp, seg_img_disp), axis=2)
ann_fmt = (font_id, loc[0], loc[1], size, thickness) + fgr_col + bgr_col
put_text_with_background(seg_img_disp, seg_labels[seg_id], fmt=ann_fmt)
seg_img_disp_list.append(seg_img_disp)
# eval_cl, _ = eval.extract_classes(seg_img)
# print('eval_cl: {}'.format(eval_cl))
if show_img:
cv2.imshow('seg_img_orig', seg_img_orig)
if len(seg_img.shape) == 3:
seg_img = seg_img[:, :, 0].squeeze()
conc_data_y = np.zeros((seg_width,), dtype=np.float64)
for i in range(seg_width):
curr_pix = np.squeeze(seg_img[:, i])
if ice_type == 0:
ice_pix = curr_pix[curr_pix != 0]
else:
ice_pix = curr_pix[curr_pix == ice_type]
conc_data_y[i] = (len(ice_pix) / float(src_height)) * 100.0
plot_cols.append(seg_col)
plot_data_y.append(conc_data_y)
if labels_path:
seg_dict = {conc_data_x[i]: conc_data_y[i] for i in range(seg_width)}
# dists['bhattacharyya'].append(bhattacharyya(gt_dict, seg_dict))
dists[_label]['euclidean'].append(euclidean(gt_dict, seg_dict))
dists[_label]['mse'].append(mse(gt_dict, seg_dict))
dists[_label]['mae'].append(mae(gt_dict, seg_dict))
# dists['frobenius'].append(np.linalg.norm(conc_data_y - plot_data_y[0]))
curr_mae_data_y.append(dists[_label]['mae'][-1])
else:
if img_id > 0:
if plot_changed_seg_count:
flow = cv2.calcOpticalFlowFarneback(prev_seg_img[_label], seg_img, None, 0.5, 3, 15, 3, 5, 1.2,
0)
print('flow: {}'.format(flow.shape))
# # Obtain the flow magnitude and direction angle
# mag, ang = cv2.cartToPolar(flow[..., 0], flow[..., 1])
# hsvImg = np.zeros((2160, 3840, 3), dtype=np.uint8)
# hsvImg[..., 1] = 255
# # Update the color image
# hsvImg[..., 0] = 0.5 * ang * 180 / np.pi
# hsvImg[..., 2] = cv2.normalize(mag, None, 0, 255, cv2.NORM_MINMAX)
# rgbImg = cv2.cvtColor(hsvImg, cv2.COLOR_HSV2BGR)
# rgbImg = resizeAR(rgbImg, width=out_width, height=out_height)
# # Display the resulting frame
# cv2.imshow('dense optical flow', rgbImg)
# k = cv2.waitKey(0)
curr_x, curr_y = (prev_x + flow[..., 0]).astype(np.int32), (prev_y + flow[..., 1]).astype(
np.int32)
seg_img_flow = seg_img[curr_y, curr_x]
changed_seg_count[_label].append(np.count_nonzero(np.not_equal(seg_img, prev_seg_img[_label])))
seg_count_data_y.append(changed_seg_count[_label])
mean_seg_counts[_label] = np.mean(changed_seg_count[_label])
else:
ice_concentration_diff[_label].append(np.mean(np.abs(conc_data_y - prev_conc_data_y[_label])))
conc_diff_data_y.append(ice_concentration_diff[_label])
mean_conc_diff[_label] = np.mean(ice_concentration_diff[_label])
else:
if plot_changed_seg_count:
prev_x, prev_y = np.meshgrid(range(seg_width), range(seg_height), sparse=False, indexing='xy')
changed_seg_count[_label] = []
else:
ice_concentration_diff[_label] = []
prev_seg_img[_label] = seg_img
prev_conc_data_y[_label] = conc_data_y
# conc_data = np.concatenate([conc_data_x, conc_data_y], axis=1)
if labels_path:
for i, k in enumerate(curr_mae_data_y):
mae_data_y[i].append(k)
n_test_images = img_id + 1
mae_data_X = np.asarray(range(1, n_test_images + 1), dtype=np.float64)
print('')
# print('mae_data_X:\n {}'.format(pformat(mae_data_X)))
# print('mae_data_y:\n {}'.format(pformat(np.array(mae_data_y).transpose())))
if img_id == end_id:
mae_data_y_arr = np.array(mae_data_y).transpose()
print('mae_data_y:\n {}'.format(tabulate(mae_data_y_arr,
headers=seg_labels, tablefmt='plain')))
pd.DataFrame(data=mae_data_y_arr, columns=seg_labels).to_clipboard(excel=True)
mae_img = getPlotImage(mae_data_X, mae_data_y, plot_cols, 'MAE', seg_labels,
'frame', 'MAE')
cv2.imshow('mae_img', mae_img)
conc_diff_img = resize_ar(mae_img, seg_width, src_height, bkg_col=255)
else:
if img_id > 0:
n_test_images = img_id
seg_count_data_X = np.asarray(range(1, n_test_images + 1), dtype=np.float64)
if plot_changed_seg_count:
seg_count_img = getPlotImage(seg_count_data_X, seg_count_data_y, plot_cols, 'Count', seg_labels,
'frame', 'Changed Label Count')
cv2.imshow('seg_count_img', seg_count_img)
else:
# print('seg_count_data_X:\n {}'.format(pformat(seg_count_data_X)))
# print('conc_diff_data_y:\n {}'.format(pformat(conc_diff_data_y)))
conc_diff_img = getPlotImage(seg_count_data_X, conc_diff_data_y, plot_cols,
'Mean concentration difference between consecutive frames'.format(
ice_type_str),
seg_labels, 'frame', 'Concentration Difference (%)')
# cv2.imshow('conc_diff_img', conc_diff_img)
conc_diff_img = resize_ar(conc_diff_img, seg_width, src_height, bkg_col=255)
else:
conc_diff_img = np.zeros((src_height, seg_width, 3), dtype=np.uint8)
plot_labels += seg_labels
if enable_plotting:
plot_img = getPlotImage(plot_data_x, plot_data_y, plot_cols, plot_title, plot_labels,
plot_x_label, plot_y_label,
legend=0
# ylim=(0, 100)
)
plot_img = resize_ar(plot_img, seg_width, src_height, bkg_col=255)
# plt.plot(conc_data_x, conc_data_y)
# plt.show()
# conc_data_fname = os.path.join(out_path, img_fname_no_ext + '.txt')
# np.savetxt(conc_data_fname, conc_data, fmt='%.6f')
ann_fmt = (font_id, loc[0], loc[1], size, thickness) + labels_col_rgb + bgr_col
put_text_with_background(src_img, 'frame {}'.format(img_id + 1), fmt=ann_fmt)
if n_seg_paths == 1:
print('seg_img_disp: {}'.format(seg_img_disp.shape))
print('plot_img: {}'.format(plot_img.shape))
stitched_seg_img = np.concatenate((seg_img_disp, plot_img), axis=1)
print('stitched_seg_img: {}'.format(stitched_seg_img.shape))
print('stitched_img: {}'.format(stitched_img.shape))
stitched_img = np.concatenate((stitched_img, stitched_seg_img), axis=0 if labels_path else 1)
elif n_seg_paths == 2:
stitched_img = np.concatenate((
np.concatenate((src_img, conc_diff_img), axis=1),
np.concatenate(seg_img_disp_list, axis=1),
), axis=0)
elif n_seg_paths == 3:
stitched_img = np.concatenate((
np.concatenate((src_img, plot_img, conc_diff_img), axis=1),
np.concatenate(seg_img_disp_list, axis=1),
), axis=0)
stitched_img = resize_ar(stitched_img, width=out_width, height=out_height)
# print('dists: {}'.format(dists))
if write_to_video:
video_out.write(stitched_img)
else:
stacked_img_path = os.path.join(stitched_seq_path, '{}.{}'.format(img_fname_no_ext, out_ext))
cv2.imwrite(stacked_img_path, stitched_img)
cv2.imshow('stitched_img', stitched_img)
k = cv2.waitKey(1 - _pause)
if k == 27:
break
elif k == 32:
_pause = 1 - _pause
end_t = time.time()
sys.stdout.write('\rDone {:d}/{:d} frames. fps: {}'.format(
img_id + 1 - start_id, n_frames, 1.0 / (end_t - start_t)))
sys.stdout.flush()
print()
if enable_plotting and write_to_video:
video_out.release()
if labels_path:
median_dists = {}
mean_dists = {}
mae_data_y = []
for _label in seg_labels:
_dists = dists[_label]
mae_data_y.append(_dists['mae'])
mean_dists[_label] = {k: np.mean(_dists[k]) for k in _dists}
median_dists[_label] = {k: np.median(_dists[k]) for k in _dists}
print('mean_dists:\n{}'.format(pformat(mean_dists)))
print('median_dists:\n{}'.format(pformat(median_dists)))
n_test_images = len(mae_data_y[0])
mae_data_x = np.asarray(range(1, n_test_images + 1), dtype=np.float64)
mae_img = getPlotImage(mae_data_x, mae_data_y, plot_cols, 'MAE', seg_labels,
'test image', 'Mean Absolute Error')
# plt.show()
cv2.imshow('MAE', mae_img)
k = cv2.waitKey(0)
else:
mean_seg_counts = {}
median_seg_counts = {}
seg_count_data_y = []
mean_conc_diff = {}
median_conc_diff = {}
conc_diff_data_y = []
for seg_id in ice_concentration_diff:
if plot_changed_seg_count:
seg_count_data_y.append(changed_seg_count[seg_id])
mean_seg_counts[seg_id] = np.mean(changed_seg_count[seg_id])
median_seg_counts[seg_id] = np.median(changed_seg_count[seg_id])
else:
_ice_concentration_diff = ice_concentration_diff[seg_id]
n_test_images = len(_ice_concentration_diff)
conc_diff_data_y.append(_ice_concentration_diff)
mean_conc_diff[seg_id] = np.mean(_ice_concentration_diff)
median_conc_diff[seg_id] = np.median(_ice_concentration_diff)
np.savetxt(os.path.join(out_path, '{}_ice_concentration_diff.txt'.format(seg_id)),
_ice_concentration_diff, fmt='%8.4f', delimiter='\t')
if plot_changed_seg_count:
print('mean_seg_counts:\n{}'.format(pformat(mean_seg_counts)))
print('median_seg_counts:\n{}'.format(pformat(median_seg_counts)))
else:
print('mean_conc_diff:')
for seg_id in mean_conc_diff:
print('{}\t{}'.format(seg_id, mean_conc_diff[seg_id]))
print('median_conc_diff:')
for seg_id in mean_conc_diff:
print('{}\t{}'.format(seg_id, median_conc_diff[seg_id]))
# seg_count_data_X = np.asarray(range(1, n_test_images + 1), dtype=np.float64)
#
# if plot_changed_seg_count:
# seg_count_img = getPlotImage(seg_count_data_X, seg_count_data_y, plot_cols, 'Count', seg_labels,
# 'test image', 'Changed Label Count')
# cv2.imshow('seg_count_img', seg_count_img)
#
# conc_diff_img = getPlotImage(seg_count_data_X, conc_diff_data_y, plot_cols, 'Difference', seg_labels,
# 'test image', 'Concentration Difference')
# cv2.imshow('conc_diff_img', conc_diff_img)
# k = cv2.waitKey(0)
if __name__ == '__main__':
main()