--- a
+++ b/monai 0.5.0/deprecated/train.py
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+# Copyright 2020 MONAI Consortium
+# 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.
+
+
+from init import Options
+from networks import *
+# from networks import build_net
+import logging
+import os
+import sys
+import tempfile
+from glob import glob
+
+import nibabel as nib
+import numpy as np
+import torch
+from torch.utils.data import DataLoader
+from torch.utils.tensorboard import SummaryWriter
+
+import monai
+from monai.data import create_test_image_3d, list_data_collate
+from monai.inferers import sliding_window_inference
+from monai.metrics import DiceMetric
+from monai.transforms import (Compose, LoadImaged, AddChanneld, Transpose,Activations,AsDiscrete, RandGaussianSmoothd, CropForegroundd, SpatialPadd,
+                              ScaleIntensityd, ToTensord, RandSpatialCropd, Rand3DElasticd, RandAffined, RandZoomd,
+    Spacingd, Orientationd, Resized, ThresholdIntensityd, RandShiftIntensityd, BorderPadd, RandGaussianNoised, RandAdjustContrastd,NormalizeIntensityd,RandFlipd)
+
+from monai.visualize import plot_2d_or_3d_image
+# from monai.engines import get_devices_spec
+
+def main():
+    opt = Options().parse()
+    # monai.config.print_config()
+    logging.basicConfig(stream=sys.stdout, level=logging.INFO)
+
+    # check gpus
+    if opt.gpu_ids != '-1':
+        num_gpus = len(opt.gpu_ids.split(','))
+    else:
+        num_gpus = 0
+    print('number of GPU:', num_gpus)
+
+    # Data loader creation
+    # train images
+    train_images = sorted(glob(os.path.join(opt.images_folder, 'train', 'image*.nii')))
+    train_segs = sorted(glob(os.path.join(opt.labels_folder, 'train', 'label*.nii')))
+
+    train_images_for_dice = sorted(glob(os.path.join(opt.images_folder, 'train', 'image*.nii')))
+    train_segs_for_dice = sorted(glob(os.path.join(opt.labels_folder, 'train', 'label*.nii')))
+
+    # validation images
+    val_images = sorted(glob(os.path.join(opt.images_folder, 'val', 'image*.nii')))
+    val_segs = sorted(glob(os.path.join(opt.labels_folder, 'val', 'label*.nii')))
+
+    # test images
+    test_images = sorted(glob(os.path.join(opt.images_folder, 'test', 'image*.nii')))
+    test_segs = sorted(glob(os.path.join(opt.labels_folder, 'test', 'label*.nii')))
+
+    # augment the data list for training
+    for i in range(int(opt.increase_factor_data)):
+
+        train_images.extend(train_images)
+        train_segs.extend(train_segs)
+
+    print('Number of training patches per epoch:', len(train_images))
+    print('Number of training images per epoch:', len(train_images_for_dice))
+    print('Number of validation images per epoch:', len(val_images))
+    print('Number of test images per epoch:', len(test_images))
+
+    # Creation of data directories for data_loader
+
+    train_dicts = [{'image': image_name, 'label': label_name}
+                  for image_name, label_name in zip(train_images, train_segs)]
+
+    train_dice_dicts = [{'image': image_name, 'label': label_name}
+                   for image_name, label_name in zip(train_images_for_dice, train_segs_for_dice)]
+
+    val_dicts = [{'image': image_name, 'label': label_name}
+                   for image_name, label_name in zip(val_images, val_segs)]
+
+    test_dicts = [{'image': image_name, 'label': label_name}
+                 for image_name, label_name in zip(test_images, test_segs)]
+
+    # Transforms list
+    # Need to concatenate multiple channels here if you want multichannel segmentation
+    # Check other examples on Monai webpage.
+
+    if opt.resolution is not None:
+        train_transforms = [
+            LoadImaged(keys=['image', 'label']),
+            AddChanneld(keys=['image', 'label']),
+            CropForegroundd(keys=['image', 'label'], source_key='image'),               # crop CropForeground
+            ThresholdIntensityd(keys=['image'], threshold=-350, above=True, cval=-350),  # Threshold CT
+            ThresholdIntensityd(keys=['image'], threshold=350, above=False, cval=350),
+
+            NormalizeIntensityd(keys=['image']),                                          # augmentation
+            ScaleIntensityd(keys=['image']),                                              # intensity
+            Spacingd(keys=['image', 'label'], pixdim=opt.resolution, mode=('bilinear', 'nearest')),  # resolution
+
+            RandFlipd(keys=['image', 'label'], prob=0.1, spatial_axis=1),
+            RandFlipd(keys=['image', 'label'], prob=0.1, spatial_axis=0),
+            RandFlipd(keys=['image', 'label'], prob=0.1, spatial_axis=2),
+            RandAffined(keys=['image', 'label'], mode=('bilinear', 'nearest'), prob=0.1,
+                        rotate_range=(np.pi / 36, np.pi / 36, np.pi * 2), padding_mode="zeros"),
+            RandAffined(keys=['image', 'label'], mode=('bilinear', 'nearest'), prob=0.1,
+                        rotate_range=(np.pi / 36, np.pi / 2, np.pi / 36), padding_mode="zeros"),
+            RandAffined(keys=['image', 'label'], mode=('bilinear', 'nearest'), prob=0.1,
+                        rotate_range=(np.pi / 2, np.pi / 36, np.pi / 36), padding_mode="zeros"),
+            Rand3DElasticd(keys=['image', 'label'], mode=('bilinear', 'nearest'), prob=0.1,
+                           sigma_range=(5, 8), magnitude_range=(100, 200), scale_range=(0.15, 0.15, 0.15),
+                           padding_mode="zeros"),
+            RandGaussianSmoothd(keys=["image"], sigma_x=(0.5, 1.15), sigma_y=(0.5, 1.15), sigma_z=(0.5, 1.15), prob=0.1,),
+            RandAdjustContrastd(keys=['image'], gamma=(0.5, 2.5), prob=0.1),
+            RandGaussianNoised(keys=['image'], prob=0.1, mean=np.random.uniform(0, 0.5), std=np.random.uniform(0, 1)),
+            RandShiftIntensityd(keys=['image'], offsets=np.random.uniform(0,0.3), prob=0.1),
+
+            SpatialPadd(keys=['image', 'label'], spatial_size=opt.patch_size, method= 'end'),  # pad if the image is smaller than patch
+            RandSpatialCropd(keys=['image', 'label'], roi_size=opt.patch_size, random_size=False),
+            ToTensord(keys=['image', 'label'])
+        ]
+
+        val_transforms = [
+            LoadImaged(keys=['image', 'label']),
+            AddChanneld(keys=['image', 'label']),
+            CropForegroundd(keys=['image', 'label'], source_key='image'),                   # crop CropForeground
+            ThresholdIntensityd(keys=['image'], threshold=-350, above=True, cval=-350),     # Threshold CT
+            ThresholdIntensityd(keys=['image'], threshold=350, above=False, cval=350),
+
+            NormalizeIntensityd(keys=['image']),                                      # intensity
+            ScaleIntensityd(keys=['image']),
+            Spacingd(keys=['image', 'label'], pixdim=opt.resolution, mode=('bilinear', 'nearest')),  # resolution
+
+            SpatialPadd(keys=['image', 'label'], spatial_size=opt.patch_size, method= 'end'),  # pad if the image is smaller than patch
+            ToTensord(keys=['image', 'label'])
+        ]
+    else:
+        train_transforms = [
+            LoadImaged(keys=['image', 'label']),
+            AddChanneld(keys=['image', 'label']),
+            CropForegroundd(keys=['image', 'label'], source_key='image'),               # crop CropForeground
+            ThresholdIntensityd(keys=['image'], threshold=-350, above=True, cval=-350),  # Threshold CT
+            ThresholdIntensityd(keys=['image'], threshold=350, above=False, cval=350),
+
+            NormalizeIntensityd(keys=['image']),                                          # augmentation
+            ScaleIntensityd(keys=['image']),                                              # intensity
+
+            RandFlipd(keys=['image', 'label'], prob=0.1, spatial_axis=1),
+            RandFlipd(keys=['image', 'label'], prob=0.1, spatial_axis=0),
+            RandFlipd(keys=['image', 'label'], prob=0.1, spatial_axis=2),
+            RandAffined(keys=['image', 'label'], mode=('bilinear', 'nearest'), prob=0.1,
+                        rotate_range=(np.pi / 36, np.pi / 36, np.pi * 2), padding_mode="zeros"),
+            RandAffined(keys=['image', 'label'], mode=('bilinear', 'nearest'), prob=0.1,
+                        rotate_range=(np.pi / 36, np.pi / 2, np.pi / 36), padding_mode="zeros"),
+            RandAffined(keys=['image', 'label'], mode=('bilinear', 'nearest'), prob=0.1,
+                        rotate_range=(np.pi / 2, np.pi / 36, np.pi / 36), padding_mode="zeros"),
+            Rand3DElasticd(keys=['image', 'label'], mode=('bilinear', 'nearest'), prob=0.1,
+                           sigma_range=(5, 8), magnitude_range=(100, 200), scale_range=(0.15, 0.15, 0.15),
+                           padding_mode="zeros"),
+            RandGaussianSmoothd(keys=["image"], sigma_x=(0.5, 1.15), sigma_y=(0.5, 1.15), sigma_z=(0.5, 1.15), prob=0.1,),
+            RandAdjustContrastd(keys=['image'], gamma=(0.5, 2.5), prob=0.1),
+            RandGaussianNoised(keys=['image'], prob=0.1, mean=np.random.uniform(0, 0.5), std=np.random.uniform(0, 1)),
+            RandShiftIntensityd(keys=['image'], offsets=np.random.uniform(0,0.3), prob=0.1),
+
+            SpatialPadd(keys=['image', 'label'], spatial_size=opt.patch_size, method= 'end'),  # pad if the image is smaller than patch
+            RandSpatialCropd(keys=['image', 'label'], roi_size=opt.patch_size, random_size=False),
+            ToTensord(keys=['image', 'label'])
+        ]
+
+        val_transforms = [
+            LoadImaged(keys=['image', 'label']),
+            AddChanneld(keys=['image', 'label']),
+            CropForegroundd(keys=['image', 'label'], source_key='image'),                   # crop CropForeground
+            ThresholdIntensityd(keys=['image'], threshold=-350, above=True, cval=-350),     # Threshold CT
+            ThresholdIntensityd(keys=['image'], threshold=350, above=False, cval=350),
+
+            NormalizeIntensityd(keys=['image']),                                      # intensity
+            ScaleIntensityd(keys=['image']),
+
+            SpatialPadd(keys=['image', 'label'], spatial_size=opt.patch_size, method= 'end'),  # pad if the image is smaller than patch
+            ToTensord(keys=['image', 'label'])
+        ]
+
+    train_transforms = Compose(train_transforms)
+    val_transforms = Compose(val_transforms)
+
+    # create a training data loader
+    check_train = monai.data.CacheDataset(data=train_dicts, transform=train_transforms)
+    train_loader = DataLoader(check_train, batch_size=opt.batch_size, shuffle=True, num_workers=opt.workers, pin_memory=torch.cuda.is_available())
+
+    # create a training_dice data loader
+    check_val = monai.data.Dataset(data=train_dice_dicts, transform=val_transforms)
+    train_dice_loader = DataLoader(check_val, batch_size=1, num_workers=opt.workers, pin_memory=torch.cuda.is_available())
+
+    # create a validation data loader
+    check_val = monai.data.Dataset(data=val_dicts, transform=val_transforms)
+    val_loader = DataLoader(check_val, batch_size=1, num_workers=opt.workers, pin_memory=torch.cuda.is_available())
+
+    # create a validation data loader
+    check_val = monai.data.Dataset(data=test_dicts, transform=val_transforms)
+    test_loader = DataLoader(check_val, batch_size=1, num_workers=opt.workers, pin_memory=torch.cuda.is_available())
+
+    # # try to use all the available GPUs
+    # devices = get_devices_spec(None)
+
+    # build the network
+    net = build_net()
+    net.cuda()
+
+    if num_gpus > 1:
+        net = torch.nn.DataParallel(net)
+
+    if opt.preload is not None:
+        net.load_state_dict(torch.load(opt.preload))
+
+    dice_metric = DiceMetric(include_background=True, reduction="mean")
+    post_trans = Compose([Activations(sigmoid=True), AsDiscrete(threshold_values=True)])
+
+    loss_function = monai.losses.DiceCELoss(sigmoid=True)
+
+    optim = torch.optim.SGD(net.parameters(), lr=opt.lr, momentum=0.99, weight_decay=3e-5, nesterov=True,)
+
+    net_scheduler = torch.optim.lr_scheduler.LambdaLR(
+        optim, lr_lambda=lambda epoch: (1 - epoch / opt.epochs) ** 0.9)
+
+    # start a typical PyTorch training
+    val_interval = 1
+    best_metric = -1
+    best_metric_epoch = -1
+    epoch_loss_values = list()
+    metric_values = list()
+    writer = SummaryWriter()
+    for epoch in range(opt.epochs):
+        print("-" * 10)
+        print(f"epoch {epoch + 1}/{opt.epochs}")
+        net.train()
+        epoch_loss = 0
+        step = 0
+        for batch_data in train_loader:
+            step += 1
+            inputs, labels = batch_data["image"].cuda(), batch_data["label"].cuda()
+            optim.zero_grad()
+            outputs = net(inputs)
+            loss = loss_function(outputs, labels)
+            loss.backward()
+            optim.step()
+            epoch_loss += loss.item()
+            epoch_len = len(check_train) // train_loader.batch_size
+            print(f"{step}/{epoch_len}, train_loss: {loss.item():.4f}")
+            writer.add_scalar("train_loss", loss.item(), epoch_len * epoch + step)
+        epoch_loss /= step
+        epoch_loss_values.append(epoch_loss)
+        print(f"epoch {epoch + 1} average loss: {epoch_loss:.4f}")
+        update_learning_rate(net_scheduler, optim)
+
+        if (epoch + 1) % val_interval == 0:
+            net.eval()
+            with torch.no_grad():
+
+                def plot_dice(images_loader):
+
+                    metric_sum = 0.0
+                    metric_count = 0
+                    val_images = None
+                    val_labels = None
+                    val_outputs = None
+                    for data in images_loader:
+                        val_images, val_labels = data["image"].cuda(), data["label"].cuda()
+                        roi_size = opt.patch_size
+                        sw_batch_size = 4
+                        val_outputs = sliding_window_inference(val_images, roi_size, sw_batch_size, net)
+                        val_outputs = post_trans(val_outputs)
+                        value, _ = dice_metric(y_pred=val_outputs, y=val_labels)
+                        metric_count += len(value)
+                        metric_sum += value.item() * len(value)
+                    metric = metric_sum / metric_count
+                    metric_values.append(metric)
+                    return metric, val_images, val_labels, val_outputs
+
+                metric, val_images, val_labels, val_outputs = plot_dice(val_loader)
+
+                # Save best model
+                if metric > best_metric:
+                    best_metric = metric
+                    best_metric_epoch = epoch + 1
+                    torch.save(net.state_dict(), "best_metric_model.pth")
+                    print("saved new best metric model")
+
+                metric_train, train_images, train_labels, train_outputs = plot_dice(train_dice_loader)
+                metric_test, test_images, test_labels, test_outputs = plot_dice(test_loader)
+
+                # Logger bar
+                print(
+                    "current epoch: {} Training dice: {:.4f} Validation dice: {:.4f} Testing dice: {:.4f} Best Validation dice: {:.4f} at epoch {}".format(
+                        epoch + 1, metric_train, metric, metric_test, best_metric, best_metric_epoch
+                    )
+                )
+
+                writer.add_scalar("Mean_epoch_loss", epoch_loss, epoch + 1)
+                writer.add_scalar("Testing_dice", metric_test, epoch + 1)
+                writer.add_scalar("Training_dice", metric_train, epoch + 1)
+                writer.add_scalar("Validation_dice", metric, epoch + 1)
+                # plot the last model output as GIF image in TensorBoard with the corresponding image and label
+                # val_outputs = (val_outputs.sigmoid() >= 0.5).float()
+                plot_2d_or_3d_image(val_images, epoch + 1, writer, index=0, tag="validation image")
+                plot_2d_or_3d_image(val_labels, epoch + 1, writer, index=0, tag="validation label")
+                plot_2d_or_3d_image(val_outputs, epoch + 1, writer, index=0, tag="validation inference")
+                plot_2d_or_3d_image(test_images, epoch + 1, writer, index=0, tag="test image")
+                plot_2d_or_3d_image(test_labels, epoch + 1, writer, index=0, tag="test label")
+                plot_2d_or_3d_image(test_outputs, epoch + 1, writer, index=0, tag="test inference")
+
+    print(f"train completed, best_metric: {best_metric:.4f} at epoch: {best_metric_epoch}")
+    writer.close()
+
+
+if __name__ == "__main__":
+    main()
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