utils.py

# Copyright (c) Microsoft Corporation
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import os
import json
import sys
import time
import numpy as np
import pandas as pd
from PIL import Image
from tqdm import tqdm
from pycocotools import mask as cocomask
from sklearn.model_selection import KFold

import settings

def create_submission(meta, predictions):
    output = []
    for image_id, mask in zip(meta['id'].values, predictions):
        rle_encoded = ' '.join(str(rle) for rle in run_length_encoding(mask))
        output.append([image_id, rle_encoded])

    submission = pd.DataFrame(output, columns=['id', 'rle_mask']).astype(str)
    return submission


def encode_rle(predictions):
    return [run_length_encoding(mask) for mask in predictions]


def read_masks(img_ids):
    masks = []
    for img_id in img_ids:
        base_filename = '{}.png'.format(img_id)
        mask = Image.open(os.path.join(settings.TRAIN_MASK_DIR, base_filename))
        mask = np.asarray(mask.convert('L').point(lambda x: 0 if x < 128 else 1)).astype(np.uint8)
        masks.append(mask)
    return masks


def run_length_encoding(x):
    bs = np.where(x.T.flatten())[0]

    rle = []
    prev = -2
    for b in bs:
        if (b > prev + 1): rle.extend((b + 1, 0))
        rle[-1] += 1
        prev = b
    return rle


def run_length_decoding(mask_rle, shape):
    s = mask_rle.split()
    starts, lengths = [np.asarray(x, dtype=int) for x in (s[0:][::2], s[1:][::2])]
    starts -= 1
    ends = starts + lengths
    img = np.zeros(shape[1] * shape[0], dtype=np.uint8)
    for lo, hi in zip(starts, ends):
        img[lo:hi] = 255
    return img.reshape((shape[1], shape[0])).T

def get_salt_existence():
    train_mask = pd.read_csv(settings.LABEL_FILE)
    salt_exists_dict = {}
    for row in train_mask.values:
        salt_exists_dict[row[0]] = 0 if (row[1] is np.nan or len(row[1]) < 1) else 1
    return salt_exists_dict

def generate_metadata(train_images_dir, test_images_dir, depths_filepath):
    depths = pd.read_csv(depths_filepath)
    salt_exists_dict = get_salt_existence()

    metadata = {}
    for filename in tqdm(os.listdir(os.path.join(train_images_dir, 'images'))):
        image_filepath = os.path.join(train_images_dir, 'images', filename)
        mask_filepath = os.path.join(train_images_dir, 'masks', filename)
        image_id = filename.split('.')[0]
        depth = depths[depths['id'] == image_id]['z'].values[0]

        metadata.setdefault('file_path_image', []).append(image_filepath)
        metadata.setdefault('file_path_mask', []).append(mask_filepath)
        metadata.setdefault('is_train', []).append(1)
        metadata.setdefault('id', []).append(image_id)
        metadata.setdefault('z', []).append(depth)
        metadata.setdefault('salt_exists', []).append(salt_exists_dict[image_id])

    for filename in tqdm(os.listdir(os.path.join(test_images_dir, 'images'))):
        image_filepath = os.path.join(test_images_dir, 'images', filename)
        image_id = filename.split('.')[0]
        depth = depths[depths['id'] == image_id]['z'].values[0]

        metadata.setdefault('file_path_image', []).append(image_filepath)
        metadata.setdefault('file_path_mask', []).append(None)
        metadata.setdefault('is_train', []).append(0)
        metadata.setdefault('id', []).append(image_id)
        metadata.setdefault('z', []).append(depth)
        metadata.setdefault('salt_exists', []).append(0)

    return pd.DataFrame(metadata)

def rle_from_binary(prediction):
    prediction = np.asfortranarray(prediction)
    return cocomask.encode(prediction)


def binary_from_rle(rle):
    return cocomask.decode(rle)


def get_segmentations(labeled):
    nr_true = labeled.max()
    segmentations = []
    for i in range(1, nr_true + 1):
        msk = labeled == i
        segmentation = rle_from_binary(msk.astype('uint8'))
        segmentation['counts'] = segmentation['counts'].decode("UTF-8")
        segmentations.append(segmentation)
    return segmentations


def get_crop_pad_sequence(vertical, horizontal):
    top = int(vertical / 2)
    bottom = vertical - top
    right = int(horizontal / 2)
    left = horizontal - right
    return (top, right, bottom, left)


def get_nfold_split(ifold, nfold=10, meta_version=1):
    if meta_version == 2:
        return get_nfold_split2(ifold, nfold)

    meta = pd.read_csv(settings.META_FILE, na_filter=False)
    meta_train = meta[meta['is_train'] == 1]

    kf = KFold(n_splits=nfold)
    for i, (train_index, valid_index) in enumerate(kf.split(meta_train[settings.ID_COLUMN].values.reshape(-1))):
        if i == ifold:
            break
    return meta_train.iloc[train_index], meta_train.iloc[valid_index]

def get_nfold_split2(ifold, nfold=10):
    meta_train = pd.read_csv(os.path.join(settings.DATA_DIR, 'train_meta2.csv'))

    with open(os.path.join(settings.DATA_DIR, 'train_split.json'), 'r') as f:
        train_splits = json.load(f)
    train_index = train_splits[str(ifold)]['train_index']
    valid_index = train_splits[str(ifold)]['val_index']

    return meta_train.iloc[train_index], meta_train.iloc[valid_index]


def get_test_meta():
    meta = pd.read_csv(settings.META_FILE, na_filter=False)
    test_meta = meta[meta['is_train'] == 0]
    print(len(test_meta.values))
    return test_meta

if __name__ == '__main__':
    get_nfold_split(2)