tune154_cls_cce.py

import os
os.environ["MKL_NUM_THREADS"] = "2" 
os.environ["NUMEXPR_NUM_THREADS"] = "2" 
os.environ["OMP_NUM_THREADS"] = "2" 

from os import path, makedirs, listdir
import sys
import numpy as np
np.random.seed(1)
import random
random.seed(1)

import torch
from torch import nn
from torch.backends import cudnn
from torch.utils.data import Dataset
from torch.utils.data import DataLoader
import torch.optim.lr_scheduler as lr_scheduler

from apex import amp

from adamw import AdamW
from losses import dice_round, ComboLoss

import pandas as pd
from tqdm import tqdm
import timeit
import cv2

from zoo.models import SeNet154_Unet_Double

from imgaug import augmenters as iaa

from utils import *

from skimage.morphology import square, dilation

from sklearn.model_selection import train_test_split

from sklearn.metrics import accuracy_score

import gc

cv2.setNumThreads(0)
cv2.ocl.setUseOpenCL(False)

train_dirs = ['train', 'tier3']

models_folder = 'weights'

loc_folder = 'pred_loc_val'

input_shape = (448, 448)


all_files = []
for d in train_dirs:
    for f in sorted(listdir(path.join(d, 'images'))):
        if '_pre_disaster.png' in f:
            all_files.append(path.join(d, 'images', f))
train_len = len(all_files)


class TrainData(Dataset):
    def __init__(self, train_idxs):
        super().__init__()
        self.train_idxs = train_idxs
        self.elastic = iaa.ElasticTransformation(alpha=(0.25, 1.2), sigma=0.2)

    def __len__(self):
        return len(self.train_idxs)

    def __getitem__(self, idx):
        _idx = self.train_idxs[idx]

        fn = all_files[_idx]

        img = cv2.imread(fn, cv2.IMREAD_COLOR)
        img2 = cv2.imread(fn.replace('_pre_', '_post_'), cv2.IMREAD_COLOR)

        msk0 = cv2.imread(fn.replace('/images/', '/masks/'), cv2.IMREAD_UNCHANGED)
        lbl_msk1 = cv2.imread(fn.replace('/images/', '/masks/').replace('_pre_disaster', '_post_disaster'), cv2.IMREAD_UNCHANGED)

        msk1 = np.zeros_like(lbl_msk1)
        msk2 = np.zeros_like(lbl_msk1)
        msk3 = np.zeros_like(lbl_msk1)
        msk4 = np.zeros_like(lbl_msk1)
        msk2[lbl_msk1 == 2] = 255
        msk3[lbl_msk1 == 3] = 255
        msk4[lbl_msk1 == 4] = 255
        msk1[lbl_msk1 == 1] = 255

        if random.random() > 0.7:
            img = img[::-1, ...]
            img2 = img2[::-1, ...]
            msk0 = msk0[::-1, ...]
            msk1 = msk1[::-1, ...]
            msk2 = msk2[::-1, ...]
            msk3 = msk3[::-1, ...]
            msk4 = msk4[::-1, ...]

        if random.random() > 0.3:
            rot = random.randrange(4)
            if rot > 0:
                img = np.rot90(img, k=rot)
                img2 = np.rot90(img2, k=rot)
                msk0 = np.rot90(msk0, k=rot)
                msk1 = np.rot90(msk1, k=rot)
                msk2 = np.rot90(msk2, k=rot)
                msk3 = np.rot90(msk3, k=rot)
                msk4 = np.rot90(msk4, k=rot)
                    
        if random.random() > 0.99:
            shift_pnt = (random.randint(-320, 320), random.randint(-320, 320))
            img = shift_image(img, shift_pnt)
            img2 = shift_image(img2, shift_pnt)
            msk0 = shift_image(msk0, shift_pnt)
            msk1 = shift_image(msk1, shift_pnt)
            msk2 = shift_image(msk2, shift_pnt)
            msk3 = shift_image(msk3, shift_pnt)
            msk4 = shift_image(msk4, shift_pnt)
            
        if random.random() > 0.5:
            rot_pnt =  (img.shape[0] // 2 + random.randint(-320, 320), img.shape[1] // 2 + random.randint(-320, 320))
            scale = 0.9 + random.random() * 0.2
            angle = random.randint(0, 20) - 10
            if (angle != 0) or (scale != 1):
                img = rotate_image(img, angle, scale, rot_pnt)
                img2 = rotate_image(img2, angle, scale, rot_pnt)
                msk0 = rotate_image(msk0, angle, scale, rot_pnt)
                msk1 = rotate_image(msk1, angle, scale, rot_pnt)
                msk2 = rotate_image(msk2, angle, scale, rot_pnt)
                msk3 = rotate_image(msk3, angle, scale, rot_pnt)
                msk4 = rotate_image(msk4, angle, scale, rot_pnt)

        crop_size = input_shape[0]
        if random.random() > 0.5:
            crop_size = random.randint(int(input_shape[0] / 1.1), int(input_shape[0] / 0.9))

        bst_x0 = random.randint(0, img.shape[1] - crop_size)
        bst_y0 = random.randint(0, img.shape[0] - crop_size)
        bst_sc = -1
        try_cnt = random.randint(1, 10)
        for i in range(try_cnt):
            x0 = random.randint(0, img.shape[1] - crop_size)
            y0 = random.randint(0, img.shape[0] - crop_size)
            _sc = msk2[y0:y0+crop_size, x0:x0+crop_size].sum() * 5 + msk3[y0:y0+crop_size, x0:x0+crop_size].sum() * 5 + msk4[y0:y0+crop_size, x0:x0+crop_size].sum() * 2 + msk1[y0:y0+crop_size, x0:x0+crop_size].sum()
            if _sc > bst_sc:
                bst_sc = _sc
                bst_x0 = x0
                bst_y0 = y0
        x0 = bst_x0
        y0 = bst_y0
        img = img[y0:y0+crop_size, x0:x0+crop_size, :]
        img2 = img2[y0:y0+crop_size, x0:x0+crop_size, :]
        msk0 = msk0[y0:y0+crop_size, x0:x0+crop_size]
        msk1 = msk1[y0:y0+crop_size, x0:x0+crop_size]
        msk2 = msk2[y0:y0+crop_size, x0:x0+crop_size]
        msk3 = msk3[y0:y0+crop_size, x0:x0+crop_size]
        msk4 = msk4[y0:y0+crop_size, x0:x0+crop_size]
        
        if crop_size != input_shape[0]:
            img = cv2.resize(img, input_shape, interpolation=cv2.INTER_LINEAR)
            img2 = cv2.resize(img2, input_shape, interpolation=cv2.INTER_LINEAR)
            msk0 = cv2.resize(msk0, input_shape, interpolation=cv2.INTER_LINEAR)
            msk1 = cv2.resize(msk1, input_shape, interpolation=cv2.INTER_LINEAR)
            msk2 = cv2.resize(msk2, input_shape, interpolation=cv2.INTER_LINEAR)
            msk3 = cv2.resize(msk3, input_shape, interpolation=cv2.INTER_LINEAR)
            msk4 = cv2.resize(msk4, input_shape, interpolation=cv2.INTER_LINEAR)
            

        if random.random() > 0.99:
            img = shift_channels(img, random.randint(-5, 5), random.randint(-5, 5), random.randint(-5, 5))
        elif random.random() > 0.99:
            img2 = shift_channels(img2, random.randint(-5, 5), random.randint(-5, 5), random.randint(-5, 5))

        if random.random() > 0.99:
            img = change_hsv(img, random.randint(-5, 5), random.randint(-5, 5), random.randint(-5, 5))
        elif random.random() > 0.99:
            img2 = change_hsv(img2, random.randint(-5, 5), random.randint(-5, 5), random.randint(-5, 5))

        if random.random() > 0.99:
            if random.random() > 0.99:
                img = clahe(img)
            elif random.random() > 0.99:
                img = gauss_noise(img)
            elif random.random() > 0.99:
                img = cv2.blur(img, (3, 3))
        elif random.random() > 0.99:
            if random.random() > 0.99:
                img = saturation(img, 0.9 + random.random() * 0.2)
            elif random.random() > 0.99:
                img = brightness(img, 0.9 + random.random() * 0.2)
            elif random.random() > 0.99:
                img = contrast(img, 0.9 + random.random() * 0.2)

        if random.random() > 0.99:
            if random.random() > 0.99:
                img2 = clahe(img2)
            elif random.random() > 0.99:
                img2 = gauss_noise(img2)
            elif random.random() > 0.99:
                img2 = cv2.blur(img2, (3, 3))
        elif random.random() > 0.99:
            if random.random() > 0.99:
                img2 = saturation(img2, 0.9 + random.random() * 0.2)
            elif random.random() > 0.99:
                img2 = brightness(img2, 0.9 + random.random() * 0.2)
            elif random.random() > 0.99:
                img2 = contrast(img2, 0.9 + random.random() * 0.2)

                
        if random.random() > 0.99:
            el_det = self.elastic.to_deterministic()
            img = el_det.augment_image(img)

        if random.random() > 0.99:
            el_det = self.elastic.to_deterministic()
            img2 = el_det.augment_image(img2)

        msk0 = msk0[..., np.newaxis]
        msk1 = msk1[..., np.newaxis]
        msk2 = msk2[..., np.newaxis]
        msk3 = msk3[..., np.newaxis]
        msk4 = msk4[..., np.newaxis]

        msk = np.concatenate([msk0, msk1, msk2, msk3, msk4], axis=2)
        msk = (msk > 127)

        msk[..., 0] = True
        msk[..., 1] = dilation(msk[..., 1], square(5))
        msk[..., 2] = dilation(msk[..., 2], square(5))
        msk[..., 3] = dilation(msk[..., 3], square(5))
        msk[..., 4] = dilation(msk[..., 4], square(5))
        msk[..., 1][msk[..., 2:].max(axis=2)] = False
        msk[..., 3][msk[..., 2]] = False
        msk[..., 4][msk[..., 2]] = False
        msk[..., 4][msk[..., 3]] = False
        msk[..., 0][msk[..., 1:].max(axis=2)] = False
        msk = msk * 1

        lbl_msk = msk.argmax(axis=2)

        img = np.concatenate([img, img2], axis=2)
        img = preprocess_inputs(img)

        img = torch.from_numpy(img.transpose((2, 0, 1))).float()
        msk = torch.from_numpy(msk.transpose((2, 0, 1))).long()

        sample = {'img': img, 'msk': msk, 'lbl_msk': lbl_msk, 'fn': fn}
        return sample


class ValData(Dataset):
    def __init__(self, image_idxs):
        super().__init__()
        self.image_idxs = image_idxs

    def __len__(self):
        return len(self.image_idxs)

    def __getitem__(self, idx):
        _idx = self.image_idxs[idx]

        fn = all_files[_idx]

        img = cv2.imread(fn, cv2.IMREAD_COLOR)
        img2 = cv2.imread(fn.replace('_pre_', '_post_'), cv2.IMREAD_COLOR)

        msk0 = cv2.imread(fn.replace('/images/', '/masks/'), cv2.IMREAD_UNCHANGED)
        lbl_msk1 = cv2.imread(fn.replace('/images/', '/masks/').replace('_pre_disaster', '_post_disaster'), cv2.IMREAD_UNCHANGED)
        msk_loc = cv2.imread(path.join(loc_folder, '{0}.png'.format(fn.split('/')[-1].replace('.png', '_part1.png'))), cv2.IMREAD_UNCHANGED) > (0.3*255)
        
        msk1 = np.zeros_like(lbl_msk1)
        msk2 = np.zeros_like(lbl_msk1)
        msk3 = np.zeros_like(lbl_msk1)
        msk4 = np.zeros_like(lbl_msk1)
        msk1[lbl_msk1 == 1] = 255
        msk2[lbl_msk1 == 2] = 255
        msk3[lbl_msk1 == 3] = 255
        msk4[lbl_msk1 == 4] = 255

        msk0 = msk0[..., np.newaxis]
        msk1 = msk1[..., np.newaxis]
        msk2 = msk2[..., np.newaxis]
        msk3 = msk3[..., np.newaxis]
        msk4 = msk4[..., np.newaxis]

        msk = np.concatenate([msk0, msk1, msk2, msk3, msk4], axis=2)
        msk = (msk > 127)

        msk = msk * 1

        lbl_msk = msk[..., 1:].argmax(axis=2)
        
        img = np.concatenate([img, img2], axis=2)
        img = preprocess_inputs(img)

        img = torch.from_numpy(img.transpose((2, 0, 1))).float()
        msk = torch.from_numpy(msk.transpose((2, 0, 1))).long()

        sample = {'img': img, 'msk': msk, 'lbl_msk': lbl_msk, 'fn': fn, 'msk_loc': msk_loc}
        return sample


def validate(net, data_loader):
    dices0 = []

    tp = np.zeros((5,))
    fp = np.zeros((5,))
    fn = np.zeros((5,))

    _thr = 0.3

    with torch.no_grad():
        for i, sample in enumerate(tqdm(data_loader)):
            msks = sample["msk"].numpy()
            lbl_msk = sample["lbl_msk"].numpy()
            imgs = sample["img"].cuda(non_blocking=True)
            msk_loc = sample["msk_loc"].numpy() * 1
            out = model(imgs)

            msk_pred = msk_loc
            msk_damage_pred = torch.softmax(out, dim=1).cpu().numpy()[:, 1:, ...]
            
            for j in range(msks.shape[0]):
                tp[4] += np.logical_and(msks[j, 0] > 0, msk_pred[j] > 0).sum()
                fn[4] += np.logical_and(msks[j, 0] < 1, msk_pred[j] > 0).sum()
                fp[4] += np.logical_and(msks[j, 0] > 0, msk_pred[j] < 1).sum()


                targ = lbl_msk[j][msks[j, 0] > 0]
                pred = msk_damage_pred[j].argmax(axis=0)
                pred = pred * (msk_pred[j] > _thr)
                pred = pred[msks[j, 0] > 0]
                for c in range(4):
                    tp[c] += np.logical_and(pred == c, targ == c).sum()
                    fn[c] += np.logical_and(pred != c, targ == c).sum()
                    fp[c] += np.logical_and(pred == c, targ != c).sum()

    d0 = 2 * tp[4] / (2 * tp[4] + fp[4] + fn[4]) 

    f1_sc = np.zeros((4,))
    for c in range(4):
        f1_sc[c] = 2 * tp[c] / (2 * tp[c] + fp[c] + fn[c])

    f1 = 4 / np.sum(1.0 / (f1_sc + 1e-6))

    sc = 0.3 * d0 + 0.7 * f1
    print("Val Score: {}, Dice: {}, F1: {}, F1_0: {}, F1_1: {}, F1_2: {}, F1_3: {}".format(sc, d0, f1, f1_sc[0], f1_sc[1], f1_sc[2], f1_sc[3]))
    return sc


def evaluate_val(data_val, best_score, model, snapshot_name, current_epoch):
    model = model.eval()
    d = validate(model, data_loader=data_val)

    if d > best_score:
        torch.save({
            'epoch': current_epoch + 1,
            'state_dict': model.state_dict(),
            'best_score': d,
        }, path.join(models_folder, snapshot_name + '_best'))
        best_score = d

    print("score: {}\tscore_best: {}".format(d, best_score))
    return best_score


def train_epoch(current_epoch, seg_loss, ce_loss, model, optimizer, scheduler, train_data_loader):
    losses = AverageMeter()
    losses1 = AverageMeter()

    dices = AverageMeter()

    iterator = tqdm(train_data_loader)
    model.train()
    for i, sample in enumerate(iterator):
        imgs = sample["img"].cuda(non_blocking=True)
        msks = sample["msk"].cuda(non_blocking=True)
        lbl_msk = sample["lbl_msk"].cuda(non_blocking=True)
        
        out = model(imgs)

        loss0 = seg_loss(out[:, 0, ...], msks[:, 0, ...])
        loss1 = seg_loss(out[:, 1, ...], msks[:, 1, ...])
        loss2 = seg_loss(out[:, 2, ...], msks[:, 2, ...])
        loss3 = seg_loss(out[:, 3, ...], msks[:, 3, ...])
        loss4 = seg_loss(out[:, 4, ...], msks[:, 4, ...])

        loss5 = ce_loss(out, lbl_msk)

        loss = 0.1 * loss0 + 0.1 * loss1 + 0.6 * loss2 + 0.3 * loss3 + 0.2 * loss4 + loss5 * 8

        with torch.no_grad():
            _probs = 1 - torch.sigmoid(out[:, 0, ...])
            dice_sc = 1 - dice_round(_probs, 1 - msks[:, 0, ...])

        losses.update(loss.item(), imgs.size(0))
        losses1.update(loss5.item(), imgs.size(0))

        dices.update(dice_sc, imgs.size(0))

        iterator.set_description(
            "epoch: {}; lr {:.7f}; Loss {loss.val:.4f} ({loss.avg:.4f}); cce_loss {loss1.val:.4f} ({loss1.avg:.4f}); Dice {dice.val:.4f} ({dice.avg:.4f})".format(
                current_epoch, scheduler.get_lr()[-1], loss=losses, loss1=losses1, dice=dices))
        
        optimizer.zero_grad()
        with amp.scale_loss(loss, optimizer) as scaled_loss:
            scaled_loss.backward()
        torch.nn.utils.clip_grad_norm_(amp.master_params(optimizer), 0.999)
        optimizer.step()

    scheduler.step(current_epoch)

    print("epoch: {}; lr {:.7f}; Loss {loss.avg:.4f}; CCE_loss {loss1.avg:.4f}; Dice {dice.avg:.4f}".format(
            current_epoch, scheduler.get_lr()[-1], loss=losses, loss1=losses1, dice=dices))


if __name__ == '__main__':
    t0 = timeit.default_timer()

    makedirs(models_folder, exist_ok=True)
    
    seed = int(sys.argv[1])
    # vis_dev = sys.argv[2]

    # os.environ['CUDA_DEVICE_ORDER'] = 'PCI_BUS_ID'
    # os.environ["CUDA_VISIBLE_DEVICES"] = vis_dev

    cudnn.benchmark = True

    batch_size = 8
    val_batch_size = 2

    snapshot_name = 'se154_cls_cce_{}_tuned'.format(seed)

    file_classes = []
    for fn in tqdm(all_files):
        fl = np.zeros((4,), dtype=bool)
        msk1 = cv2.imread(fn.replace('/images/', '/masks/').replace('_pre_disaster', '_post_disaster'), cv2.IMREAD_UNCHANGED)
        for c in range(1, 5):
            fl[c-1] = c in msk1
        file_classes.append(fl)
    file_classes = np.asarray(file_classes)

    _, val_idxs = train_test_split(np.arange(train_len), test_size=0.1, random_state=seed)

    np.random.seed(seed + 531)
    random.seed(seed + 531)

    train_idxs = []
    for i in np.arange(len(all_files)):
        train_idxs.append(i)
        if file_classes[i, 1:].max():
            train_idxs.append(i)
    train_idxs = np.asarray(train_idxs)

    steps_per_epoch = len(train_idxs) // batch_size
    validation_steps = len(val_idxs) // val_batch_size

    print('steps_per_epoch', steps_per_epoch, 'validation_steps', validation_steps)

    data_train = TrainData(train_idxs)
    val_train = ValData(val_idxs)

    train_data_loader = DataLoader(data_train, batch_size=batch_size, num_workers=6, shuffle=True, pin_memory=False, drop_last=True)
    val_data_loader = DataLoader(val_train, batch_size=val_batch_size, num_workers=6, shuffle=False, pin_memory=False)

    model = SeNet154_Unet_Double().cuda()

    params = model.parameters()

    optimizer = AdamW(params, lr=0.000008, weight_decay=1e-6)
    
    model, optimizer = amp.initialize(model, optimizer, opt_level="O1")

    scheduler = lr_scheduler.MultiStepLR(optimizer, milestones=[1, 2, 3, 4, 5, 7, 9, 11, 17, 23, 29, 33, 47, 50, 60, 70, 90, 110, 130, 150, 170, 180, 190], gamma=0.5)

    model = nn.DataParallel(model).cuda()

    snap_to_load = 'se154_cls_cce_{}_1_best'.format(seed)
    print("=> loading checkpoint '{}'".format(snap_to_load))
    checkpoint = torch.load(path.join(models_folder, snap_to_load), map_location='cpu')
    loaded_dict = checkpoint['state_dict']
    sd = model.state_dict()
    for k in model.state_dict():
        if k in loaded_dict and sd[k].size() == loaded_dict[k].size():
            sd[k] = loaded_dict[k]
    loaded_dict = sd
    model.load_state_dict(loaded_dict)
    print("loaded checkpoint '{}' (epoch {}, best_score {})"
            .format(snap_to_load, checkpoint['epoch'], checkpoint['best_score']))
    del loaded_dict
    del sd
    del checkpoint
    gc.collect()
    torch.cuda.empty_cache()

    seg_loss = ComboLoss({'dice': 0.5}, per_image=False).cuda()
    ce_loss = nn.CrossEntropyLoss().cuda()

    best_score = 0
    torch.cuda.empty_cache()
    for epoch in range(2):
        train_epoch(epoch, seg_loss, ce_loss, model, optimizer, scheduler, train_data_loader)
        torch.cuda.empty_cache()
        best_score = evaluate_val(val_data_loader, best_score, model, snapshot_name, epoch)

    elapsed = timeit.default_timer() - t0
    print('Time: {:.3f} min'.format(elapsed / 60))