train_lt_mxp.py

import sys, json, os, argparse, time
from operator import itemgetter
import shutil
import os.path as osp
from datetime import datetime
import operator
from tqdm import trange
import numpy as np
import torch
import torch.nn.functional as F
from models.get_model import get_arch
from utils.get_loaders import get_train_val_cls_loaders, modify_dataset, modify_loader, get_combo_loader

from utils.evaluation import evaluate_multi_cls
from utils.model_saving_loading import save_model, str2bool, load_model
from utils.reproducibility import set_seeds

from torch.optim.lr_scheduler import ReduceLROnPlateau
from typing import Tuple

# argument parsing
parser = argparse.ArgumentParser()
# as seen here: https://stackoverflow.com/a/15460288/3208255
# parser.add_argument('--layers',  nargs='+', type=int, help='unet configuration (depth/filters)')
# annoyingly, this does not get on well with guild.ai, so we need to reverse to this one:

parser.add_argument('--csv_train', type=str, default='data/train_eyepacs.csv', help='path to training data csv')
parser.add_argument('--data_path', type=str, default='data/eyepacs_all_ims/', help='path data')
parser.add_argument('--sampling', type=str, default='instance', help='sampling mode (instance, class, sqrt, prog)')
parser.add_argument('--model_name', type=str, default='bit_resnext50_1', help='architecture')
parser.add_argument('--n_classes', type=int, default=5, help='binary disease detection (1) or multi-class (5)')
parser.add_argument('--loss_fn', type=str, default='ce', help='loss function (ce)')
parser.add_argument('--do_mixup', type=float, default=0.0, help='mixup coeff (so far only for multi-class')
parser.add_argument('--batch_size', type=int, default=8, help='batch size')
parser.add_argument('--optimizer', type=str, default='sgd', help='optimizer choice')
parser.add_argument('--patience', type=int, default=2, help='patience before lr reduction')
parser.add_argument('--lr', type=float, default=0.01, help='learning rate')
parser.add_argument('--min_lr', type=float, default=-1, help='learning rate (defaults to stopping just after 3rd decay)')
parser.add_argument('--wd', type=float, default=0, help='weight decay')
parser.add_argument('--n_epochs', type=int, default=7, help='nr epochs') #
parser.add_argument('--metric', type=str, default='auc', help='which metric to use for monitoring progress (loss/dice)')
parser.add_argument('--im_size', help='delimited list input, could be 500, or 600,400', type=str, default='512,512')
parser.add_argument('--pretrained_weights', type=str, default=None, help='start from eyepacs-pretrained weights (path to)')
parser.add_argument('--do_not_save', type=str2bool, nargs='?', const=True, default=False, help='avoid saving anything')
parser.add_argument('--save_path', type=str, default='date_time', help='path to save model (defaults to date/time')
parser.add_argument('--num_workers', type=int, default=8, help='number of parallel (multiprocessing) workers to launch '
                                                               'for data loading tasks (handled by pytorch) [default: %(default)s]')
parser.add_argument('--n_checkpoints', type=int, default=1, help='nr of best checkpoints to keep (defaults to 3)')

def sgd_optimizer(model, lr, momentum, weight_decay):
    params = []
    for key, value in model.named_parameters():
        if not value.requires_grad:
            continue
        apply_weight_decay = weight_decay
        apply_lr = lr
        if 'bias' in key or 'bn' in key:
            apply_weight_decay = 0
            # print('set weight decay=0 for {}'.format(key))
        if 'bias' in key:
            apply_lr = 2 * lr       #   Just a Caffe-style common practice. Made no difference.
        params += [{'params': [value], 'lr': apply_lr, 'weight_decay': apply_weight_decay}]
    optimizer = torch.optim.SGD(params, lr, momentum=momentum)
    return optimizer

def compare_op(metric):
    '''
    This should return an operator that given a, b returns True if a is better than b
    Also, let us return which is an appropriately terrible initial value for such metric
    '''
    if metric == 'auc':
        return operator.gt, 0
    elif metric == 'mcc':
        return operator.gt, 0
    elif metric == 'kappa':
        return operator.gt, 0
    elif metric == 'f1':
        return operator.gt, 0
    elif metric == 'bacc':
        return operator.gt, 0
    elif metric == 'loss':
        return operator.lt, np.inf
    else:
        raise NotImplementedError

def get_lr(optimizer):
    for param_group in optimizer.param_groups:
        return param_group['lr']

def partial_mixup(input: torch.Tensor,
                  gamma: float,
                  indices: torch.Tensor
                  ) -> torch.Tensor:
    if input.size(0) != indices.size(0):
        raise RuntimeError("Size mismatch!")
    perm_input = input[indices]
    return input.mul(gamma).add(perm_input, alpha=1 - gamma)


def mixup(input: torch.Tensor,
          target: torch.Tensor,
          gamma: float,
          ) -> Tuple[torch.Tensor, torch.Tensor]:
    indices = torch.randperm(input.size(0), device=input.device, dtype=torch.long)
    return partial_mixup(input, gamma, indices), partial_mixup(target, gamma, indices)

def cross_entropy_loss(input: torch.Tensor,
                             target: torch.Tensor
                             ) -> torch.Tensor:
    return -(input.log_softmax(dim=-1) * target).sum(dim=-1).mean()

def run_one_epoch(loader, model, criterion, do_mixup=0., optimizer=None, assess=False):

    device='cuda' if next(model.parameters()).is_cuda else 'cpu'
    train = optimizer is not None  # if we are in training mode there will be an optimizer and train=True here
    n_classes = model.n_classes

    if train: model.train()
    else: model.eval()
    if assess:
        probs_all, preds_all, labels_all = [], [], []

    with trange(len(loader)) as t:
        n_elems, running_loss = 0, 0

        for i_batch, batch in enumerate(loader):
            if train:
                lam = np.random.beta(a=do_mixup, b=1)

                inputs, labels = batch[0][0], batch[0][1]
                balanced_inputs, balanced_labels = batch[1][0], batch[1][1]

                inputs, labels = inputs.to(device), labels.squeeze().to(device)
                balanced_inputs, balanced_labels = balanced_inputs.to(device), balanced_labels.squeeze().to(device)


                inputs = (1 - lam) * inputs + lam * balanced_inputs
                mixed_labels = (1 - lam) * F.one_hot(labels, n_classes) + lam * F.one_hot(balanced_labels, n_classes)

                del balanced_inputs
                del balanced_labels
            else:
                inputs, labels = batch[0].to(device), batch[1].squeeze().to(device)

            logits = model(inputs)
            loss = cross_entropy_loss(logits, mixed_labels) if train else criterion(logits, labels)

            if train:  # only in training mode
                loss.backward()
                optimizer.step()
                optimizer.zero_grad()

            if assess:
                probs = logits.softmax(dim=1)
                preds = np.argmax(probs.detach().cpu().numpy(), axis=1)
                probs_all.extend(probs.detach().cpu().numpy())
                preds_all.extend(preds)
                labels_all.extend(labels.cpu().numpy())

            # Compute running loss
            running_loss += loss.detach().item() * inputs.size(0)
            n_elems += inputs.size(0)
            run_loss = running_loss / n_elems
            if train: t.set_postfix(loss_lr="{:.4f}/{:.6f}".format(float(run_loss), get_lr(optimizer)))
            else: t.set_postfix(vl_loss="{:.4f}".format(float(run_loss)))
            t.update()

    if assess: return np.stack(preds_all), np.stack(probs_all), np.stack(labels_all), run_loss
    return None, None, None, None

def train_model(model, sampling, optimizer, train_criterion, val_criterion, do_mixup, train_loader, val_loader,
                scheduler, metric, n_epochs, exp_path, n_checkpoints):

    best_loss, best_auc, best_bacc, best_k, best_mcc, best_f1, best_epoch, best_models = 10, 0, 0, 0, 0, 0, 0, []
    is_better, best_monitoring_metric = compare_op(metric)
    greater_is_better = best_monitoring_metric == 0
    all_tr_aucs, all_vl_aucs, all_tr_mccs, all_vl_mccs = [], [], [], []
    all_tr_ks, all_vl_ks, all_tr_baccs, all_vl_baccs, all_tr_losses, all_vl_losses = [], [], [], [], [], []

    if model.n_classes == 5: class_names = ['DR0', 'DR1', 'DR2', 'DR3', 'DR4']
    else: class_names = ['C{}'.format(i) for i in range(model.n_classes)]
    print_conf, text_file_train, text_file_val = False, None, None

    for epoch in range(n_epochs):
        print('\nEpoch {:d}/{:d}'.format(epoch+1, n_epochs))
        # Modify sampling
        combo_loader = get_combo_loader(train_loader, base_sampling=sampling)
        # train one epoch
        _, _, _, _ = run_one_epoch(combo_loader, model, train_criterion, do_mixup, optimizer, assess=True)

        with torch.no_grad():
            tr_preds, tr_probs, tr_labels, tr_loss = run_one_epoch(train_loader, model, val_criterion, assess=True)
            vl_preds, vl_probs, vl_labels, vl_loss = run_one_epoch(val_loader, model, val_criterion, assess=True)


        if exp_path is not None:
            print_conf = True
            text_file_train = osp.join(exp_path,'performance_epoch_{}.txt'.format(str(epoch+1).zfill(2)))
            text_file_val = osp.join(exp_path, 'performance_epoch_{}.txt'.format(str(epoch+1).zfill(2)))

        tr_auc, tr_k, tr_mcc, tr_f1, tr_bacc, tr_auc_all, tr_f1_all = evaluate_multi_cls(tr_labels, tr_preds, tr_probs, print_conf=print_conf,
                                                              class_names=class_names, text_file=text_file_train, loss=tr_loss)
        vl_auc, vl_k, vl_mcc, vl_f1, vl_bacc, vl_auc_all, vl_f1_all = evaluate_multi_cls(vl_labels, vl_preds, vl_probs, print_conf=print_conf,
                                                              class_names=class_names, text_file=text_file_val, loss=vl_loss, lr=get_lr(optimizer))

        print('Train||Val Loss: {:.4f}||{:.4f} - K: {:.2f}||{:.2f} - mAUC: {:.2f}||{:.2f} - MCC: {:.2f}||{:.2f} - BACC: {:.2f}||{:.2f}'.format(
            tr_loss, vl_loss, 100 * tr_k, 100 * vl_k, 100 * tr_auc, 100 * vl_auc, 100 * tr_mcc, 100 * vl_mcc, 100 * tr_bacc, 100 * vl_bacc))

        all_tr_aucs.append(tr_auc_all)
        all_vl_aucs.append(vl_auc_all)
        all_tr_mccs.append(tr_mcc)
        all_vl_mccs.append(vl_mcc)
        all_tr_baccs.append(tr_bacc)
        all_vl_baccs.append(vl_bacc)
        all_tr_ks.append(tr_k)
        all_vl_ks.append(vl_k)
        all_tr_losses.append(tr_loss)
        all_vl_losses.append(vl_loss)

        # check if performance was better than anyone before and checkpoint if so
        if metric == 'loss':  tr_monitoring_metric, vl_monitoring_metric  = tr_loss, vl_loss
        elif metric == 'kappa': tr_monitoring_metric, vl_monitoring_metric  =  tr_k, vl_k
        elif metric == 'mcc': tr_monitoring_metric, vl_monitoring_metric  =  tr_mcc, vl_mcc
        elif metric == 'f1':  tr_monitoring_metric, vl_monitoring_metric  =  tr_f1, vl_f1
        elif metric == 'auc': tr_monitoring_metric, vl_monitoring_metric  =  tr_auc, vl_auc
        elif metric == 'bacc': tr_monitoring_metric, vl_monitoring_metric = tr_bacc, vl_bacc

        if tr_monitoring_metric > vl_monitoring_metric:  # only if we do not underfit
            scheduler.step(vl_monitoring_metric)

        if is_better(vl_monitoring_metric, best_monitoring_metric):
            print('-------- Best {} attained. {:.2f} --> {:.2f} --------'.format(metric, 100*best_monitoring_metric, 100*vl_monitoring_metric))
            best_loss, best_k, best_mcc, best_f1, best_auc, best_bacc, best_epoch = vl_loss, vl_k, vl_mcc, vl_f1, vl_auc, vl_bacc, epoch+1
            best_monitoring_metric = vl_monitoring_metric
        else:
            print('-------- Best {} so far {:.2f} at epoch {:d} --------'.format(metric, 100 * best_monitoring_metric,
                                                                                 best_epoch))

        # SAVE n best - keep deleting worse ones
        if exp_path is not None:
            s_name = 'epoch_{}_K_{:.2f}_mAUC_{:.2f}_MCC_{:.2f}'.format(str(epoch + 1).zfill(2), 100 * vl_k,
                                                                       100 * vl_auc, 100 * vl_mcc)
            best_models.append([osp.join(exp_path, s_name), vl_monitoring_metric])

            if epoch < n_checkpoints:  # first n_checkpoints epochs save always
                print('-------- Checkpointing to {}/ --------'.format(s_name))
                save_model(osp.join(exp_path, s_name), model, optimizer, weights=True)
            else:
                worst_model = sorted(best_models, key=itemgetter(1), reverse=greater_is_better)[-1][
                    0]  # False for Loss, True for K
                if s_name != worst_model:  # this model was better than one of the best n_checkpoints models, remove that one
                    print('-------- Checkpointing to {}/ --------'.format(s_name))
                    save_model(osp.join(exp_path, s_name), model, optimizer, weights=True)
                    # print('before deleting', os.listdir(osp.join(exp_path, s_name)))
                    print('----------- Deleting {}/ -----------'.format(worst_model.split('/')[-1]))
                    shutil.rmtree(worst_model)
                    best_models = sorted(best_models, key=itemgetter(1), reverse=greater_is_better)[:n_checkpoints]

        if np.isclose(get_lr(optimizer), scheduler.min_lrs[0]):
            print('Early stopping')
            del model
            torch.cuda.empty_cache()
            return best_auc, best_bacc, best_mcc, best_k, all_tr_aucs, all_vl_aucs, all_tr_mccs, all_vl_mccs, \
                   all_tr_ks, all_vl_ks, all_tr_losses, all_vl_losses, best_epoch

    del model
    torch.cuda.empty_cache()
    return best_auc, best_bacc, best_mcc, best_k, all_tr_aucs, all_vl_aucs, all_tr_mccs, all_vl_mccs, \
           all_tr_ks, all_vl_ks, all_tr_losses, all_vl_losses, best_epoch


if __name__ == '__main__':

    args = parser.parse_args()


    use_cuda = torch.cuda.is_available()
    device = torch.device("cuda:0" if use_cuda else "cpu")

    # reproducibility
    seed_value = 0
    set_seeds(seed_value, use_cuda)

    data_path = args.data_path
    n_classes = args.n_classes

    # gather parser parameters
    sampling = args.sampling
    model_name = args.model_name
    optimizer_choice = args.optimizer
    lr, min_lr, patience, bs = args.lr, args.min_lr, args.patience, args.batch_size
    if min_lr == -1: min_lr = lr * 1e-3

    n_epochs, metric = args.n_epochs, args.metric

    im_size = tuple([int(item) for item in args.im_size.split(',')])
    if isinstance(im_size, tuple) and len(im_size)==1:
        tg_size = (im_size[0], im_size[0])
    elif isinstance(im_size, tuple) and len(im_size)==2:
        tg_size = (im_size[0], im_size[1])
    else:
        sys.exit('im_size should be a number or a tuple of two numbers')

    do_not_save = str2bool(args.do_not_save)
    if do_not_save is False:
        save_path = args.save_path
        if save_path == 'date_time':
            save_path = datetime.now().strftime("%Y-%m-%d-%H:%M:%S")
        experiment_path=osp.join('experiments', save_path)
        args.experiment_path = experiment_path
        os.makedirs(experiment_path, exist_ok=True)
        n_checkpoints = args.n_checkpoints
        config_file_path = osp.join(experiment_path,'config.cfg')
        with open(config_file_path, 'w') as f:
            json.dump(vars(args), f, indent=2)
    else: experiment_path, n_checkpoints=None, 0

    csv_train = args.csv_train
    csv_val = csv_train.replace('train', 'val')

    print('* Instantiating a {} model'.format(model_name))
    model, mean, std = get_arch(model_name, n_classes=n_classes)
    print('* Creating Dataloaders, batch size = {}, workers = {}'.format(bs, args.num_workers))
    train_loader, val_loader = get_train_val_cls_loaders(csv_path_train=csv_train, csv_path_val=csv_val,
                                                         data_path=data_path, batch_size=bs,
                                                         tg_size=tg_size, mean=mean, std=std,
                                                         num_workers=args.num_workers)
    model = model.to(device)

    print("Total params: {0:,}".format(sum(p.numel() for p in model.parameters() if p.requires_grad)))
    if optimizer_choice == 'adam':
        optimizer = torch.optim.Adam(model.parameters(), lr=lr)
    elif optimizer_choice == 'sgd':
        optimizer = torch.optim.SGD(model.parameters(), lr=lr, weight_decay=args.wd)
    else:
        sys.exit('please choose a valid optimizer')

    if args.pretrained_weights is True:
        weights_path = osp.join('data/pretrained_weights/', model_name)
        try:
            model, stats, optimizer_state_dict = load_model(model, args.resume_path, device=device, with_opt=True)
            optimizer.load_state_dict(optimizer_state_dict)
        except:
            sys.exit('Pretrained weights not compatible for this model')
        for i, param_group in enumerate(optimizer.param_groups):
            param_group['lr'] = lr

    scheduler = ReduceLROnPlateau(optimizer,  mode='max', factor=0.1, patience=patience, min_lr=min_lr, verbose=False)

    train_criterion, val_criterion = torch.nn.CrossEntropyLoss(), torch.nn.CrossEntropyLoss()
    do_mixup = args.do_mixup

    print('* Instantiating loss function', str(train_criterion))
    print('* Starting to train\n','-' * 10)
    start = time.time()
    b_mauc, b_bacc, b_mcc, b_k, tr_aucs, vl_aucs, \
    tr_mccs, vl_mccs, tr_ks, vl_ks, tr_ls, vl_ls, b_epoch = train_model(model, sampling, optimizer, train_criterion, val_criterion,
                                                                        do_mixup, train_loader, val_loader, scheduler,
                                                                        metric, n_epochs, experiment_path, n_checkpoints)

    end = time.time()
    hours, rem = divmod(end - start, 3600)
    minutes, seconds = divmod(rem, 60)
    print("b_mauc: %f" % b_mauc)
    print("b_mcc: %f" % b_mcc)
    print("b_k: %f" % b_k)
    print("b_epoch: %d" % b_epoch)

    if do_not_save is False:
        with open(osp.join(experiment_path, 'val_metrics.txt'), 'w') as f:
            print(
                'Best K = {:.2f}\nBest mAUC = {:.2f}\nBest MCC = {:.2f}\nBest BACC = {:.2f}\nBest epoch = {}\n'.format(
                    100 * b_k, 100 * b_mauc, 100 * b_mcc, 100 * b_bacc, b_epoch), file=f)
            for j in range(len(vl_aucs)):
                print(
                    'Epoch = {} -> K={:.2f}/{:.2f}, mAUC={:.2f}/{:.2f}, MCC={:.2f}/{:.2f}, Loss={:.4f}/{:.4f},'.format(
                        j + 1, 100 * tr_ks[j], 100 * vl_ks[j],
                        100 * np.mean(tr_aucs[j]), 100 * np.mean(vl_aucs[j]),
                        100 * tr_mccs[j], 100 * vl_mccs[j], tr_ls[j], vl_ls[j]), file=f)

            print('\nTraining time: {:0>2}h {:0>2}min {:05.2f}secs'.format(int(hours), int(minutes), seconds), file=f)