def test_npy_pickle(self):
test_data = {"test": np.random.randint(0, 256, size=[3, 4, 4])}
with tempfile.TemporaryDirectory() as tempdir:
filepath = os.path.join(tempdir, "test_data.npy")
np.save(filepath, test_data, allow_pickle=True)
result = LoadNumpy(data_only=True, dtype=None)(filepath).item()
self.assertTupleEqual(result["test"].shape, test_data["test"].shape)
np.testing.assert_allclose(result["test"], test_data["test"])
def test_npz1(self):
test_data1 = np.random.randint(0, 256, size=[3, 4, 4])
with tempfile.TemporaryDirectory() as tempdir:
filepath = os.path.join(tempdir, "test_data.npy")
np.save(filepath, test_data1)
result = LoadNumpy()(filepath)
self.assertTupleEqual(result[1]["spatial_shape"], test_data1.shape)
self.assertTupleEqual(result[0].shape, test_data1.shape)
np.testing.assert_allclose(result[0], test_data1)
def test_npy_pickle(self):
test_data = {"test": np.random.randint(0, 256, size=[3, 4, 4])}
tempdir = tempfile.mkdtemp()
filepath = os.path.join(tempdir, "test_data.npy")
np.save(filepath, test_data, allow_pickle=True)
result = LoadNumpy(data_only=True, dtype=None)(filepath).item()
self.assertTupleEqual(result["test"].shape, test_data["test"].shape)
np.testing.assert_allclose(result["test"], test_data["test"])
shutil.rmtree(tempdir)
def test_npz1(self):
test_data1 = np.random.randint(0, 256, size=[3, 4, 4])
tempdir = tempfile.mkdtemp()
filepath = os.path.join(tempdir, "test_data.npy")
np.save(filepath, test_data1)
result = LoadNumpy()(filepath)
self.assertTupleEqual(result[1]["spatial_shape"], test_data1.shape)
self.assertTupleEqual(result[0].shape, test_data1.shape)
np.testing.assert_allclose(result[0], test_data1)
shutil.rmtree(tempdir)
def test_npz3(self):
test_data1 = np.random.randint(0, 256, size=[3, 4, 4])
test_data2 = np.random.randint(0, 256, size=[3, 4, 4])
with tempfile.TemporaryDirectory() as tempdir:
filepath = os.path.join(tempdir, "test_data.npz")
np.savez(filepath, test1=test_data1, test2=test_data2)
result = LoadNumpy(npz_keys=["test1", "test2"])(filepath)
self.assertTupleEqual(result[1]["spatial_shape"], test_data1.shape)
self.assertTupleEqual(result[0].shape, (2, 3, 4, 4))
np.testing.assert_allclose(result[0],
np.stack([test_data1, test_data2]))
def main():
monai.config.print_config()
logging.basicConfig(stream=sys.stdout, level=logging.INFO)
# --------------- Dataset ---------------
datadir1 = "/home1/quanquan/datasets/lsw/benign_65/fpAML_55/slices/"
image_files = np.array([x.path for x in os.scandir(datadir1+"image") if x.name.endswith(".npy")])
label_files = np.array([x.path for x in os.scandir(datadir1+"label") if x.name.endswith(".npy")])
image_files.sort()
label_files.sort()
# --- ??? what's up ???
train_files = [{"img":img, "seg":seg} for img, seg in zip(image_files[:-20], label_files[:-20])]
val_files = [{"img":img, "seg":seg} for img, seg in zip(image_files[-20:], label_files[-20:])]
# print("files", train_files[:20])
# print(val_files)
val_imtrans = Compose([LoadNumpy(data_only=True), ScaleIntensity(), AddChannel(), ToTensor()])
val_segtrans = Compose([LoadNumpy(data_only=True), AddChannel(), ToTensor()])
# define array dataset, data loader
check_ds = ArrayDataset(image_files, train_imtrans, label_files, train_segtrans)
check_loader = DataLoader(check_ds, batch_size=10, num_workers=2, pin_memory=torch.cuda.is_available())
im, seg = monai.utils.misc.first(check_loader)
print(im.shape, seg.shape)
# create a training data loader
train_ds = ArrayDataset(image_files[:-20], train_imtrans, label_files[:-20], train_segtrans)
train_loader = DataLoader(train_ds, batch_size=4, shuffle=True, num_workers=8, pin_memory=torch.cuda.is_available())
# create a validation data loader
val_ds = ArrayDataset(image_files[-20:], val_imtrans, label_files[-20:], val_segtrans)
val_loader = DataLoader(val_ds, batch_size=1, num_workers=4, pin_memory=torch.cuda.is_available())
dice_metric = DiceMetric(include_background=True, reduction="mean")
post_trans = Compose([Activations(sigmoid=True), AsDiscrete(threshold_values=True)])
# --------------- model ---------------
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
model = monai.networks.nets.UNet(
dimensions=2,
in_channels=1,
out_channels=1,
channels=(16, 32, 64, 128, 256),
strides=(2, 2, 2, 2),
num_res_units=2,
).to(device)
# --------------- loss function ---------------
loss_function = monai.losses.DiceLoss(sigmoid=True)
optimizer = torch.optim.Adam(model.parameters(), 1e-3)
val_interval = 1
best_metric = -1
best_metric_epoch = -1
epoch_loss_values = list()
metric_values = list()
# writer = SummaryWriter(logdir=tdir(output_dir, "sumamry"))
# ------------------- Training ----------------------
for epoch in range(max_epoch):
# print("-" * 10)
# print(f"epoch {epoch + 1}/{10}")
model.train()
epoch_loss = 0
step = 0
for batch_data in train_loader:
step += 1
inputs, labels = batch_data[0].to(device), batch_data[1].to(device)
optimizer.zero_grad()
outputs = model(inputs)
loss = loss_function(outputs, labels)
loss.backward()
optimizer.step()
epoch_loss += loss.item()
epoch_len = len(train_ds) // train_loader.batch_size
print(f"\r\t Training batch: {step}/{epoch_len}, \ttrain_loss: {loss.item():.4f}\t", end="")
writer.add_scalar("train_loss", loss.item(), epoch_len * epoch + step)
epoch_loss /= step
epoch_loss_values.append(epoch_loss)
print(f"\n\tepoch {epoch + 1} \taverage loss: {epoch_loss:.4f}")
# ------------------- Save Model ----------------------
if epoch % 5 == 0:
def get_lr(optimizer):
for param_group in optimizer.param_groups:
return float(param_group['lr'])
state = {'epoch': epoch + 1,
'lr': get_lr(optimizer),
'model_state': model.state_dict(),
'optimizer_state': optimizer.state_dict()
}
torch.save(state, tfilename(output_dir, "model", "{}_{}.pkl".format("lsw_monai_simple", epoch)))
# ------------------- Evaluation -----------------------
if (epoch + 1) % val_interval == 0:
model.eval()
with torch.no_grad():
metric_sum = 0.0
metric_count = 0
val_images = None
val_labels = None
val_outputs = None
for val_data in val_loader:
val_images, val_labels = val_data[0].to(device), val_data[1].to(device)
roi_size = (96, 96)
sw_batch_size = 4
val_outputs = sliding_window_inference(val_images, roi_size, sw_batch_size, model)
val_outputs = post_trans(val_outputs)
# value, _ = dice_metric(y_pred=val_outputs, y=val_labels)
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)
if metric > best_metric:
best_metric = metric
best_metric_epoch = epoch + 1
torch.save(model.state_dict(), "best_metric_model_segmentation2d_array.pth")
print("saved new best metric model")
print(
"current epoch: {} current mean dice: {:.4f} best mean dice: {:.4f} at epoch {}".format(
epoch + 1, metric, best_metric, best_metric_epoch
)
)
writer.add_scalar("val_mean_dice", metric, epoch + 1)
# plot the last model output as GIF image in TensorBoard with the corresponding image and label
plot_2d_or_3d_image(val_images, epoch + 1, writer, index=0, tag="image")
plot_2d_or_3d_image(val_labels, epoch + 1, writer, index=0, tag="label")
plot_2d_or_3d_image(val_outputs, epoch + 1, writer, index=0, tag="output")
print(f"train completed, best_metric: {best_metric:.4f} at epoch: {best_metric_epoch}")
writer.close()
from monai.data import ArrayDataset, create_test_image_2d
from monai.inferers import sliding_window_inference
from monai.metrics import DiceMetric
from monai.transforms import Activations, AddChannel, AsDiscrete, Compose, LoadImage, RandRotate90, RandSpatialCrop, ScaleIntensity, ToTensor, LoadNumpy
from monai.visualize import plot_2d_or_3d_image
import numpy as np
from tutils import *
# --------------- hyper-params -------------------------
output_dir = tdir("output/seg-monai-simple/", generate_name())
writer = SummaryWriter(tdir(output_dir, "summary"))
max_epoch = 200
train_imtrans = Compose(
[
LoadNumpy(data_only=True),
ScaleIntensity(),
AddChannel(),
RandSpatialCrop((96, 96), random_size=False),
RandRotate90(prob=0.5, spatial_axes=(0, 1)),
ToTensor(),
]
)
train_segtrans = Compose(
[
LoadNumpy(data_only=True),
AddChannel(),
RandSpatialCrop((96, 96), random_size=False),
RandRotate90(prob=0.5, spatial_axes=(0, 1)),
ToTensor(),
]