040_augumentation_yellow.py

# !/usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2021 Luca Clissa, Marco Dalla, Roberto Morelli
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

"""
Created on Tue May  7 10:42:13 2019
@author: Roberto Morelli
"""

import glob
import sys
import numpy as np
import imageio
import cv2
import random
from skimage import transform
import os
from tqdm import tqdm
from subprocess import check_output
import matplotlib.pyplot as plt
from importlib import import_module
from skimage import io
import skimage.io
from skimage.transform import rotate
from skimage.transform import resize
from subprocess import check_output
import albumentations as alb
from scipy import ndimage
import matplotlib.pyplot as plt
from skimage.morphology import watershed, remove_small_holes, remove_small_objects, label, erosion
from skimage.feature import peak_local_max
import argparse
import logging
import shutil

from albumentations import (RandomCrop,CenterCrop,ElasticTransform,RGBShift,Rotate,
    Compose, ToFloat, FromFloat, RandomRotate90, Flip, OneOf, MotionBlur, MedianBlur, Blur,Transpose,
    ShiftScaleRotate, OpticalDistortion, GridDistortion, RandomBrightnessContrast, VerticalFlip, HorizontalFlip,

    HueSaturationValue,
)

from augmentation_utils import *
from config import *
from utils import *

image_ids = os.listdir(CropImages)
image_ids.sort()
shift = len(image_ids)
id_edges = [300, 302, 1161, 1380, 1908, 2064] #These numbers are valid if use our test

if __name__ == "__main__":

    try:
        with open('id_new_images.pickle', 'rb') as handle:
            dic = pickle.load(handle)
        id_new_images = dic['id_new_images']
    except:
        id_new_images = int(0.8*shift)

    print(id_new_images)

    parser = argparse.ArgumentParser(description='Define augmentation setting....default mode to follow the paper description')
    parser.add_argument('--start_from_zero',action='store_true', help='remove previous file in the destination folder')

    parser.add_argument('--split_num', nargs="?", type=int, default=4, help='augmentation factor for the images segmented automatically')
    parser.add_argument('--split_num_new_images', nargs="?", type=int, default=10, help='augmentation factor fot the images segmented manually')

    parser.add_argument('--no_copy_images', action='store_const', const=True, default=False,
                        help='copy cropped in crop_aug images')
    parser.add_argument('--no_copy_masks', action='store_const', const=True, default=False,
                        help='copy cropped in crop_aug masks')

    parser.add_argument('--unique_split', type=int, default=0,
                        help='default is 0, define a different number and the same split factor will be used for all the images (automatically and manually segmented)')
    parser.add_argument('--no_artifact_aug', action='store_const', const=True, default=False,
                        help='run basic augmentation')

    args = parser.parse_args()

    if args.start_from_zero:
        print('deleting existing files in destination folder')
        if (args.no_artifact_aug) | (args.unique_split):
            try:
                shutil.rmtree(AugCropImagesBasic)
            except:
                pass
            os.makedirs(AugCropImagesBasic,exist_ok=True)
            try:
                shutil.rmtree(AugCropMasksBasic)
            except:
                pass
            os.makedirs(AugCropMasksBasic,exist_ok=True)
            path_images = AugCropImagesBasic
            path_masks = AugCropMasksBasic
        else:
            try:
                shutil.rmtree(AugCropImages)
            except:
                pass
            os.makedirs(AugCropImages,exist_ok=True)
            try:
                shutil.rmtree(AugCropMasks)
            except:
                pass
            os.makedirs(AugCropMasks,exist_ok=True)
            path_images = AugCropImages
            path_masks = AugCropMasks

    src_files = os.listdir(CropImages)
    # src_files_i.sort()
    # src_files_m = os.listdir(CropWeightedMasks)
    # src_files_m.sort()

    # limits = min((len(src_files_i), len(src_files_m)))

    if not args.no_copy_images:
        print('copying images')
        for file_name in src_files:
            full_file_name = os.path.join(CropImages, file_name)
            if os.path.isfile(full_file_name):
                shutil.copy(full_file_name, path_images)

    if not args.no_copy_masks:
        print('copying masks')
        for file_name in src_files:
            full_file_name = os.path.join(CropWeightedMasks, file_name)
            if os.path.isfile(full_file_name):
                shutil.copy(full_file_name, path_masks)

    make_data_augmentation(image_ids, CropImages,  CropWeightedMasks, args.split_num, id_new_images,
                           args.split_num_new_images, id_edges, path_images, path_masks,  shift
                           , args.unique_split, args.no_artifact_aug
                           )