RuntimeError: ignore_index is not supported for floating point target


I’m new to Pytorch and I’m trying to perform semantic segmentation of 3d images. When I use cross entropy loss with ignore index, I get the above error.

def training_fn(net,
                epochs: int = 1,
                batch_size: int = 1,
                learning_rate: float = 1e-3,
                save_checkpoint: bool = True):
    # create dataset
    dataset = hdf5.Hdf5Dataset(data_file_path, image_dim=input_dim, contains_mask=True)

    # create training and validation dataset
    n_dataset = dataset.__len__()
    n_val = round(n_dataset * valiation_percent)
    n_train = n_dataset - n_val
    train_set, val_set = random_split(dataset, [n_train, n_val])

    # create dataloaders
    train_dataloader = DataLoader(train_set, shuffle=True, batch_size=batch_size, num_workers=1, pin_memory=True)
    val_dataloader = DataLoader(val_set, shuffle=False, batch_size=batch_size, num_workers=1, pin_memory=True)

    # specify loss functions, optimizers
    loss_fn = nn.CrossEntropyLoss(ignore_index=2)
    optimizer = torch.optim.Adam(net.parameters(), lr=learning_rate)
    scheduler = lr_scheduler.StepLR(optimizer, step_size=10, gamma=0.1)

    for epoch in range(1, epochs + 1):
        print('Epoch {}/{}'.format(epoch, epochs))
        print('-' * 10)
        if os.path.exists(checkpoint_path):  # checking if there is a file with this name
            checkpoint = torch.load(checkpoint_path)
        # scheduler.step()
        for param_group in optimizer.param_groups:
            print("LR", param_group['lr'])
        running_loss = 0
        i = 0
        # training
        for batch in train_dataloader:
            image = batch[0]
            image = image.permute(1, 0, 2, 3)
            true_mask = batch[1]
            image =, dtype=torch.float32)
            true_mask =, dtype=torch.int64)
            true_mask = F.one_hot(true_mask, config.n_classes)
            true_mask = true_mask.permute(0, 1, 4, 2, 3)
            true_mask = true_mask[-1, :, :, :]
            true_mask = true_mask.type(torch.float32)


            pred = net(image)

            # pred = pred.permute(1, 0, 2, 3)
            loss = loss_fn(torch.round(pred), torch.round(true_mask))
            i += 1
            # Backpropagation


            running_loss += loss.item()
            # print(f'Accuracy score, Hamming loss - : {mIoU(pred, true_mask)}')
            if (i == n_train):
                print(f'Epoch : {epoch},  loss: {(running_loss / i):.4f}')

I have three labels - 0, 1, 2. I tried to round values so that it would be integer, but it is not working. Any suggestions would be helpful.

Hi Vasudha!

CrossEntropyLoss works in two different ways.

For your semantic-segmentation use case, the input (the prediction
made by your model) would typically have shape
[nBatch, nClass, height, width, depth].

Case 1: Your ground-truth labels – the target passed to
CrossEntropyLoss – are integer categorical class labels, and will have
shape [nBatch, height, width, depth] (with no nClass dimension).
This case supports ignore_index.

Case 2: target consists of floating-point probabilistic (“soft”) labels, and
has shape [nBatch, nClass, height, width, depth]. This case does
not support ignore_index (because there really isn’t a notion of a class
“index,” i.e., an integer class label).

If you wish to use ignore_index you need to convert your labels to long()
(not just round them to floating-point values that are integers) and ensure
that your labels tensor (target) does not have an nClass dimension.


K. Frank

Hi Frank,

Thanks for the reply.

After converting to long, I still get the same error.

I have batch size as 1 and since images are large, I interchanged the depth to batch size and input size is - [depth, nBatch, height, width] and the target is of the form [depth, nClass, height, width]. Ground truth is in the same dimension as output. I’m not sure how to remove the nClass from the target so that all layers will be compared. Hope I’m clear about the dimensions.

True mask torch.Size([16, 3, 256, 256])
Image - torch.Size([16, 1, 256, 256])
Pred shape - torch.Size([16, 3, 256, 256])


Hi Frank,

Just an update, I removed the nClass from both target and ground truth and I still get the same error.

            pred = net(image)
            pred = pred[:,-1,:,:]
            pred_ = pred.type(torch.LongTensor)
            print(f'Pred shape - {pred_.shape}')
            loss = loss_fn(pred_,true_mask)
True mask torch.Size([16, 256, 256])
Image - torch.Size([16, 1, 256, 256])
Pred shape - torch.Size([16, 256, 256])
Traceback (most recent call last):
  File "", line 164, in <module>
  File "", line 86, in training_fn
    loss = loss_fn(pred_,true_mask)
  File "/env/lib/python3.7/site-packages/torch/nn/modules/", line 1110, in _call_impl
    return forward_call(*input, **kwargs)
  File "/env/lib/python3.7/site-packages/torch/nn/modules/", line 1165, in forward
  File "/env/lib/python3.7/site-packages/torch/nn/", line 2996, in cross_entropy
    return torch._C._nn.cross_entropy_loss(input, target, weight, _Reduction.get_enum(reduction), ignore_index, label_smoothing)
RuntimeError: ignore_index is not supported for floating point target

Hi Vasudha!

You don’t have the requirements for pred and mask correct yet.

Your pred (target for CrossEntropyLoss) has to be floating-point and
have an nClass dimension, while mask (target for CrossEntropyLoss)
has to be long() and not have the nClass dimension.


>>> import torch
>>> torch.__version__
>>> _ = torch.manual_seed (2022)
>>> pred = torch.randn (1, 3, 256, 256, 16)       # pred is floating-point and has nClass dimension
>>> mask = torch.randint (3, (1, 256, 256, 16))   # mask is integer and does not have nClass dimension
>>> torch.nn.CrossEntropyLoss (ignore_index = 2) (pred, mask)


K. Frank

It is working now. Thank you.