def show_images_and_masks(imagesdir,
masksdir,
suffix='_mask',
show=False,
save=False):
all_images = get_subfiles(imagesdir)
for imagefilename in all_images:
filename = imagefilename.split('.')[0]
maskfilename = str(filename) + suffix + '.png'
img = cv2.imread(imagesdir + '/' + imagefilename)
mask = cv2.imread(masksdir + '/' + maskfilename)
if os.getenv('COLORMAP_FLAG').upper() == 'TRUE':
mask_modified = apply_color_map(mask)
else:
mask_modified = get_binary_image(mask)
combined_img = np.concatenate((img, mask_modified), axis=1)
if show:
cv2.imshow("annotations - Filename: {}".format(filename),
combined_img)
cv2.waitKey()
cv2.destroyAllWindows()
if save:
cv2.imwrite('results/combined/{}'.format(str(filename) + '.png'),
combined_img)
def save_images_and_masks(imagesdir, masksdir, suffix='_predict', show=False,
save=False):
all_mask_images = get_subfiles(masksdir)
counter = 1
for maskfilename in all_mask_images:
image_id = maskfilename.split('.')[0].replace(suffix, '')
imagefilename = image_id + '.jpg'
img = cv2.imread(imagesdir + '/' + imagefilename)
mask = cv2.imread(masksdir + '/' + maskfilename)
if os.getenv('COLORMAP_FLAG').upper() == 'TRUE':
mask_modified = apply_color_map(mask)
else:
mask_modified = get_binary_image(mask)
combined_img = np.concatenate((img, mask_modified), axis=1)
if show:
cv2.imshow("annotations - Filename: {}".format(image_id), combined_img)
cv2.waitKey()
cv2.destroyAllWindows()
if save:
print('\ncounter: {}'.format(counter))
print('results/combined/{}'.format(str(image_id) + '.png'))
cv2.imwrite(os.path.join(os.getenv('COMBINED_IMAGES_PATH'), (str(image_id) + '.png')), combined_img)
counter += 1
def test_generator(test_path, target_size=(256, 256), flag_multi_class=False, as_gray=True):
test_images_filename = get_subfiles(test_path)
for i in range(len(test_images_filename)):
imgrgb = io.imread(os.path.join(test_path, test_images_filename[i]))
if as_gray:
img = rgb2gray(imgrgb)
img = trans.resize(img, target_size)
img = np.reshape(img, img.shape+(1,)) if (not flag_multi_class) else img
img = np.reshape(img, (1,)+img.shape)
yield img
def train_valid_test_split(master_data_path,
train_path,
valid_path,
test_path,
percent_valid=0.2,
percent_test=0.2):
# distribute files from master to train, valid and test
all_data_filenames = get_subfiles(os.path.join(master_data_path, 'images'))
valid_filenames = random.sample(
all_data_filenames,
int((percent_valid / 100.0) * len(all_data_filenames)))
test_filenames = random.sample(
valid_filenames, int((percent_test / 100.0) * len(valid_filenames)))
train_filenames = [
x for x in all_data_filenames if x not in valid_filenames
]
valid_filenames = [x for x in valid_filenames if x not in test_filenames]
# create directories
create_directory(train_path)
create_directory(os.path.join(train_path, 'images'))
create_directory(os.path.join(train_path, 'masks'))
create_directory(test_path)
create_directory(os.path.join(test_path, 'png_images'))
create_directory(os.path.join(test_path, 'tiff_images'))
create_directory(valid_path)
create_directory(os.path.join(valid_path, 'images'))
create_directory(os.path.join(valid_path, 'masks'))
# copy train files
for file in train_filenames:
copyfile(os.path.join(os.path.join(master_data_path, 'images'), file),
os.path.join(os.path.join(train_path, 'images'), file))
mask_filename = file.split('.')[0] + '_mask.png'
copyfile(
os.path.join(os.path.join(master_data_path, 'masks'),
mask_filename),
os.path.join(os.path.join(train_path, 'masks'), mask_filename))
print('\nTrain files copied successfully ...')
# copy validation files
for file in valid_filenames:
copyfile(os.path.join(os.path.join(master_data_path, 'images'), file),
os.path.join(os.path.join(valid_path, 'images'), file))
mask_filename = file.split('.')[0] + '_mask.png'
copyfile(
os.path.join(os.path.join(master_data_path, 'masks'),
mask_filename),
os.path.join(os.path.join(valid_path, 'masks'), mask_filename))
print('\nValidation files copied successfully ...')
# copy test files
for file in test_filenames:
copyfile(os.path.join(os.path.join(master_data_path, 'images'), file),
os.path.join(os.path.join(test_path, 'png_images'), file))
copyfile(
os.path.join(cropped_tiff_images_path,
file.split('.')[0] + '.tif'),
os.path.join(os.path.join(test_path, 'tiff_images'),
file.split('.')[0] + '.tif'))
print('\nTest files copied successfully ...')