Issue
I am trying to implement a SimCLR/Resnet18 model with a custom dataset.
My training dataset used for pretext tasks is composed of 7000 with various unlabeled types of pictures, all aggregated in train_X_v1.bin, of shape (7000, 3, 224, 224).
For the fine tuning I have two files val_hiv_ni_X_v1.bin which contains the pictures I want to tune my model on, of shape (931, 3, 224, 224), and val_hiv_ni_y_v1.bin which contains the corresponding labels of shape: (931,).
My pretext task is supposedly already "dummy-trained" (quick training of 10 epochs just to see if the code runs) and saved in a checkpoint.
Here is my code for fine tuning :
def reproducibility(config):
SEED = int(config.seed)
torch.manual_seed(SEED)
torch.backends.cudnn.deterministic = True
torch.backends.cudnn.benchmark = False
np.random.seed(SEED)
if (config.cuda):
torch.cuda.manual_seed(SEED)
# From https://github.com/PyTorchLightning/pytorch-lightning/issues/924
def weights_update(model, checkpoint_path):
checkpoint = torch.load(checkpoint_path)
model_dict = model.state_dict()
pretrained_dict = {k: v for k, v in checkpoint['state_dict'].items() if k in model_dict}
model_dict.update(pretrained_dict)
model.load_state_dict(model_dict)
print(f'Checkpoint {checkpoint_path} was loaded')
return model
def get_idr_dataloader(batch_size, transform=None, split="unlabeled"):
# idr = STL10("./", split=split, transform=transform, download=True)
idr = ImageDataResourceDataset(root=SOURCE_PATH, transform=Augment(224), split=split)
print(idr.data.shape, idr.labels.shape)
return DataLoader(dataset=idr, batch_size=batch_size, num_workers=cpu_count() // 2, ) # cpu_count() // 2
# general stuff
available_gpus = len([torch.cuda.device(i) for i in range(torch.cuda.device_count())])
train_config = FtHparams()
save_model_path = os.path.join(os.getcwd(), "saved_models/")
print('available_gpus:', available_gpus)
filename = 'SimCLR_ResNet18_finetune_'
reproducibility(train_config)
save_name = filename + '_Final.ckpt'
# load resnet backbone
backbone = models.resnet18(pretrained=False)
backbone.fc = nn.Identity()
checkpoint = torch.load('resnet18_backbone_weights.ckpt')
backbone.load_state_dict(checkpoint['model_state_dict'])
model = SimCLR_eval(train_config.lr, model=backbone, linear_eval=False)
# preprocessing and data loaders
transform_preprocess = Augment(train_config.img_size).test_transform
data_loader = get_idr_dataloader(train_config.batch_size, transform=transform_preprocess, split='unlabeled')
data_loader_test = get_idr_dataloader(train_config.batch_size, transform=transform_preprocess, split='test')
# callbacks and trainer
accumulator = GradientAccumulationScheduler(scheduling={0: train_config.gradient_accumulation_steps})
checkpoint_callback = ModelCheckpoint(filename=filename, dirpath=save_model_path, save_last=True, save_top_k=2,
monitor='Val Accuracy_epoch', mode='max')
trainer = Trainer(callbacks=[checkpoint_callback, accumulator],
gpus=available_gpus,
max_epochs=train_config.epochs)
trainer.fit(model, data_loader, data_loader_test)
trainer.save_checkpoint(save_name)
"""# Finetune from Imageget pretraining"""
# load model
resnet = models.resnet18(pretrained=False)
resnet.fc = nn.Identity()
print('imagenet weights, no pretraining')
model = SimCLR_eval(train_config.lr, model=resnet, linear_eval=False)
# preprocessing and data loaders
transform_preprocess = Augment(train_config.img_size).test_transform
data_loader = get_idr_dataloader(70, transform=transform_preprocess, split='unlabeled')
data_loader_test = get_idr_dataloader(70, transform=transform_preprocess, split='test')
checkpoint_callback = ModelCheckpoint(filename=filename, dirpath=save_model_path)
trainer = Trainer(callbacks=[checkpoint_callback],
gpus=available_gpus,
max_epochs=train_config.epochs)
trainer.fit(model, data_loader, data_loader_test)
trainer.save_checkpoint(save_name)
Here are my classes :
class SimCLR_eval(pl.LightningModule):
def __init__(self, lr, model=None, linear_eval=False):
super().__init__()
self.lr = lr
self.linear_eval = linear_eval
if self.linear_eval:
model.eval()
self.mlp = torch.nn.Sequential(
torch.nn.Linear(512, 10),
# torch.nn.ReLU(),
# torch.nn.Dropout(0.1),
# torch.nn.Linear(128, 10)
)
self.model = torch.nn.Sequential(
model, self.mlp
)
self.loss = torch.nn.CrossEntropyLoss()
def forward(self, X):
return self.model(X)
def training_step(self, batch, batch_idx):
x, y = batch
z = self.forward(x)
loss = self.loss(z, y)
self.log('Cross Entropy loss', loss, on_step=True, on_epoch=True, prog_bar=True, logger=True)
predicted = z.argmax(1)
acc = (predicted == y).sum().item() / y.size(0)
self.log('Train Acc', acc, on_step=False, on_epoch=True, prog_bar=True, logger=True)
return loss
def validation_step(self, batch, batch_idx):
x, y = batch
z = self.forward(x)
loss = self.loss(z, y)
self.log('Val CE loss', loss, on_step=True, on_epoch=True, prog_bar=False, logger=True)
predicted = z.argmax(1)
acc = (predicted == y).sum().item() / y.size(0)
self.log('Val Accuracy', acc, on_step=True, on_epoch=True, prog_bar=True, logger=True)
return loss
def configure_optimizers(self):
if self.linear_eval:
print(f"\n\n Attention! Linear evaluation \n")
optimizer = SGD(self.mlp.parameters(), lr=self.lr, momentum=0.9)
else:
optimizer = SGD(self.model.parameters(), lr=self.lr, momentum=0.9)
return [optimizer]
class FtHparams:
def __init__(self):
self.epochs = 10 # number of training epochs
self.seed = 77777 # randomness seed
self.cuda = False # use nvidia gpu
self.img_size = 224 # image shape
self.save = "./saved_models/" # save checkpoint
self.gradient_accumulation_steps = 1 # gradient accumulation steps
self.batch_size = 70
self.lr = 1e-3
self.embedding_size = 128 # papers value is 128
self.temperature = 0.5 # 0.1 or 0.5
class ImageDataResourceDataset(VisionDataset):
train_list = ['train_X_v1.bin', ]
test_list = ['val_hiv_ni_X_v1.bin', 'val_hiv_ni_y_v1.bin', ]
def __init__(self, root: str, split: str = 'unlabeled', transform: Optional[Callable] = None, ):
super().__init__(root=root, transform=transform)
if split == 'unlabeled':
self.data, _ = self.__loadfile(self.train_list[0])
self.labels = np.asarray([-1] * self.data.shape[0])
elif split == 'test':
self.data, self.labels = self.__loadfile(self.test_list[0], self.test_list[1])
def __len__(self) -> int:
return self.data.shape[0]
def __getitem__(self, idx):
img = self.data[idx]
img = np.transpose(img, (1, 2, 0))
img = Image.fromarray(img)
img = self.transform(img)
return img
def __loadfile(self, data_file: str, labels_file: Optional[str] = None) -> Tuple[np.ndarray, Optional[np.ndarray]]:
labels = None
if labels_file:
path_to_labels = os.path.join(os.getcwd(), 'datasets', labels_file)
with open(path_to_labels, "rb") as f:
labels = np.fromfile(f, dtype=np.uint8) # 0-based
path_to_data = os.path.join(os.getcwd(), 'datasets', data_file)
everything = np.fromfile(path_to_data, dtype=np.uint8)
images = np.reshape(everything, (-1, 3, 224, 224))
images = np.transpose(images, (0, 1, 3, 2))
return images, labels
class ContrastiveLoss(nn.Module):
"""
Vanilla Contrastive loss, also called InfoNceLoss as in SimCLR paper
"""
def __init__(self, batch_size, temperature=0.5):
super().__init__()
self.batch_size = batch_size
self.temperature = temperature
self.mask = (~torch.eye(batch_size * 2, batch_size * 2, dtype=bool)).float()
def calc_similarity_batch(self, a, b):
representations = torch.cat([a, b], dim=0)
similarity_matrix = F.cosine_similarity(representations.unsqueeze(1), representations.unsqueeze(0), dim=2)
return similarity_matrix
def forward(self, proj_1, proj_2):
"""
proj_1 and proj_2 are batched embeddings [batch, embedding_dim]
where corresponding indices are pairs
z_i, z_j in the SimCLR paper
"""
batch_size = proj_1.shape[0]
z_i = F.normalize(proj_1, p=2, dim=1)
z_j = F.normalize(proj_2, p=2, dim=1)
similarity_matrix = self.calc_similarity_batch(z_i, z_j)
sim_ij = torch.diag(similarity_matrix, batch_size)
sim_ji = torch.diag(similarity_matrix, -batch_size)
positives = torch.cat([sim_ij, sim_ji], dim=0)
nominator = torch.exp(positives / self.temperature)
# print(" sim matrix ", similarity_matrix.shape)
# print(" device ", device_as(self.mask, similarity_matrix).shape, " torch exp ", torch.exp(similarity_matrix / self.temperature).shape)
denominator = device_as(self.mask, similarity_matrix) * torch.exp(similarity_matrix / self.temperature)
all_losses = -torch.log(nominator / torch.sum(denominator, dim=1))
loss = torch.sum(all_losses) / (2 * self.batch_size)
return loss
And here is my full stack trace :
/home/wlutz/PycharmProjects/hiv-image-analysis/venv/bin/python /home/wlutz/PycharmProjects/hiv-image-analysis/main.py
2023-10-25 13:59:41.831899: I tensorflow/core/util/port.cc:111] oneDNN custom operations are on. You may see slightly different numerical results due to floating-point round-off errors from different computation orders. To turn them off, set the environment variable `TF_ENABLE_ONEDNN_OPTS=0`.
2023-10-25 13:59:41.834073: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used.
2023-10-25 13:59:41.861845: E tensorflow/compiler/xla/stream_executor/cuda/cuda_dnn.cc:9342] Unable to register cuDNN factory: Attempting to register factory for plugin cuDNN when one has already been registered
2023-10-25 13:59:41.861869: E tensorflow/compiler/xla/stream_executor/cuda/cuda_fft.cc:609] Unable to register cuFFT factory: Attempting to register factory for plugin cuFFT when one has already been registered
2023-10-25 13:59:41.861884: E tensorflow/compiler/xla/stream_executor/cuda/cuda_blas.cc:1518] Unable to register cuBLAS factory: Attempting to register factory for plugin cuBLAS when one has already been registered
2023-10-25 13:59:41.867193: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 AVX512F AVX512_VNNI FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
2023-10-25 13:59:42.564010: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
/home/wlutz/PycharmProjects/hiv-image-analysis/venv/lib/python3.9/site-packages/pl_bolts/__init__.py:11: FutureWarning: In the future `np.object` will be defined as the corresponding NumPy scalar.
if not hasattr(numpy, tp_name):
/home/wlutz/PycharmProjects/hiv-image-analysis/venv/lib/python3.9/site-packages/pl_bolts/__init__.py:11: FutureWarning: In the future `np.bool` will be defined as the corresponding NumPy scalar.
if not hasattr(numpy, tp_name):
/home/wlutz/PycharmProjects/hiv-image-analysis/venv/lib/python3.9/site-packages/pl_bolts/models/self_supervised/amdim/amdim_module.py:34: UnderReviewWarning: The feature generate_power_seq is currently marked under review. The compatibility with other Lightning projects is not guaranteed and API may change at any time. The API and functionality may change without warning in future releases. More details: https://lightning-bolts.readthedocs.io/en/latest/stability.html
"lr_options": generate_power_seq(LEARNING_RATE_CIFAR, 11),
/home/wlutz/PycharmProjects/hiv-image-analysis/venv/lib/python3.9/site-packages/pl_bolts/models/self_supervised/amdim/amdim_module.py:92: UnderReviewWarning: The feature FeatureMapContrastiveTask is currently marked under review. The compatibility with other Lightning projects is not guaranteed and API may change at any time. The API and functionality may change without warning in future releases. More details: https://lightning-bolts.readthedocs.io/en/latest/stability.html
contrastive_task: Union[FeatureMapContrastiveTask] = FeatureMapContrastiveTask("01, 02, 11"),
/home/wlutz/PycharmProjects/hiv-image-analysis/venv/lib/python3.9/site-packages/pl_bolts/losses/self_supervised_learning.py:228: UnderReviewWarning: The feature AmdimNCELoss is currently marked under review. The compatibility with other Lightning projects is not guaranteed and API may change at any time. The API and functionality may change without warning in future releases. More details: https://lightning-bolts.readthedocs.io/en/latest/stability.html
self.nce_loss = AmdimNCELoss(tclip)
/home/wlutz/PycharmProjects/hiv-image-analysis/venv/lib/python3.9/site-packages/torchvision/models/_utils.py:208: UserWarning: The parameter 'pretrained' is deprecated since 0.13 and may be removed in the future, please use 'weights' instead.
warnings.warn(
/home/wlutz/PycharmProjects/hiv-image-analysis/venv/lib/python3.9/site-packages/torchvision/models/_utils.py:223: UserWarning: Arguments other than a weight enum or `None` for 'weights' are deprecated since 0.13 and may be removed in the future. The current behavior is equivalent to passing `weights=None`.
warnings.warn(msg)
available_gpus: 0
/home/wlutz/PycharmProjects/hiv-image-analysis/venv/lib/python3.9/site-packages/pytorch_lightning/trainer/connectors/accelerator_connector.py:478: LightningDeprecationWarning: Setting `Trainer(gpus=0)` is deprecated in v1.7 and will be removed in v2.0. Please use `Trainer(accelerator='gpu', devices=0)` instead.
rank_zero_deprecation(
GPU available: False, used: False
TPU available: False, using: 0 TPU cores
IPU available: False, using: 0 IPUs
HPU available: False, using: 0 HPUs
/home/wlutz/PycharmProjects/hiv-image-analysis/venv/lib/python3.9/site-packages/pytorch_lightning/callbacks/model_checkpoint.py:613: UserWarning: Checkpoint directory /home/wlutz/PycharmProjects/hiv-image-analysis/saved_models exists and is not empty.
rank_zero_warn(f"Checkpoint directory {dirpath} exists and is not empty.")
| Name | Type | Params
-------------------------------------------
0 | mlp | Sequential | 5.1 K
1 | model | Sequential | 11.2 M
2 | loss | CrossEntropyLoss | 0
-------------------------------------------
11.2 M Trainable params
0 Non-trainable params
11.2 M Total params
44.727 Total estimated model params size (MB)
Sanity Checking DataLoader 0: 0%| | 0/2 [00:00<?, ?it/s]Traceback (most recent call last):
File "/home/wlutz/PycharmProjects/hiv-image-analysis/main.py", line 253, in <module>
finetuning()
File "/home/wlutz/PycharmProjects/hiv-image-analysis/main.py", line 226, in finetuning
trainer.fit(model, data_loader, data_loader_test)
File "/home/wlutz/PycharmProjects/hiv-image-analysis/venv/lib/python3.9/site-packages/pytorch_lightning/trainer/trainer.py", line 608, in fit
call._call_and_handle_interrupt(
File "/home/wlutz/PycharmProjects/hiv-image-analysis/venv/lib/python3.9/site-packages/pytorch_lightning/trainer/call.py", line 38, in _call_and_handle_interrupt
return trainer_fn(*args, **kwargs)
File "/home/wlutz/PycharmProjects/hiv-image-analysis/venv/lib/python3.9/site-packages/pytorch_lightning/trainer/trainer.py", line 650, in _fit_impl
self._run(model, ckpt_path=self.ckpt_path)
File "/home/wlutz/PycharmProjects/hiv-image-analysis/venv/lib/python3.9/site-packages/pytorch_lightning/trainer/trainer.py", line 1112, in _run
results = self._run_stage()
File "/home/wlutz/PycharmProjects/hiv-image-analysis/venv/lib/python3.9/site-packages/pytorch_lightning/trainer/trainer.py", line 1191, in _run_stage
self._run_train()
File "/home/wlutz/PycharmProjects/hiv-image-analysis/venv/lib/python3.9/site-packages/pytorch_lightning/trainer/trainer.py", line 1204, in _run_train
self._run_sanity_check()
File "/home/wlutz/PycharmProjects/hiv-image-analysis/venv/lib/python3.9/site-packages/pytorch_lightning/trainer/trainer.py", line 1276, in _run_sanity_check
val_loop.run()
File "/home/wlutz/PycharmProjects/hiv-image-analysis/venv/lib/python3.9/site-packages/pytorch_lightning/loops/loop.py", line 199, in run
self.advance(*args, **kwargs)
File "/home/wlutz/PycharmProjects/hiv-image-analysis/venv/lib/python3.9/site-packages/pytorch_lightning/loops/dataloader/evaluation_loop.py", line 152, in advance
dl_outputs = self.epoch_loop.run(self._data_fetcher, dl_max_batches, kwargs)
File "/home/wlutz/PycharmProjects/hiv-image-analysis/venv/lib/python3.9/site-packages/pytorch_lightning/loops/loop.py", line 199, in run
self.advance(*args, **kwargs)
File "/home/wlutz/PycharmProjects/hiv-image-analysis/venv/lib/python3.9/site-packages/pytorch_lightning/loops/epoch/evaluation_epoch_loop.py", line 137, in advance
output = self._evaluation_step(**kwargs)
File "/home/wlutz/PycharmProjects/hiv-image-analysis/venv/lib/python3.9/site-packages/pytorch_lightning/loops/epoch/evaluation_epoch_loop.py", line 234, in _evaluation_step
output = self.trainer._call_strategy_hook(hook_name, *kwargs.values())
File "/home/wlutz/PycharmProjects/hiv-image-analysis/venv/lib/python3.9/site-packages/pytorch_lightning/trainer/trainer.py", line 1494, in _call_strategy_hook
output = fn(*args, **kwargs)
File "/home/wlutz/PycharmProjects/hiv-image-analysis/venv/lib/python3.9/site-packages/pytorch_lightning/strategies/strategy.py", line 390, in validation_step
return self.model.validation_step(*args, **kwargs)
File "/home/wlutz/PycharmProjects/hiv-image-analysis/finetuning.py", line 65, in validation_step
loss = self.loss(z, y)
File "/home/wlutz/PycharmProjects/hiv-image-analysis/venv/lib/python3.9/site-packages/torch/nn/modules/module.py", line 1518, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
File "/home/wlutz/PycharmProjects/hiv-image-analysis/venv/lib/python3.9/site-packages/torch/nn/modules/module.py", line 1527, in _call_impl
return forward_call(*args, **kwargs)
File "/home/wlutz/PycharmProjects/hiv-image-analysis/venv/lib/python3.9/site-packages/torch/nn/modules/loss.py", line 1179, in forward
return F.cross_entropy(input, target, weight=self.weight,
File "/home/wlutz/PycharmProjects/hiv-image-analysis/venv/lib/python3.9/site-packages/torch/nn/functional.py", line 3053, in cross_entropy
return torch._C._nn.cross_entropy_loss(input, target, weight, _Reduction.get_enum(reduction), ignore_index, label_smoothing)
RuntimeError: 0D or 1D target tensor expected, multi-target not supported
Process finished with exit code 1
I saw in the PyTorch forum that the model output is expected to be (batch size, n classes) and target (batch size) for the contrastive loss. On the last line of error, the parameter input has a shape of torch.Size([70, 10]) and target has a shape of torch.Size([70, 3, 224, 224]). so it seems targets does not meet the expectations of torch._C._nn.cross_entropy_loss ??
I'm so lost, thank you for your help.
EDIT: I forgot to specify that I have only two classes for my fine tuning
Solution
I think that you are attempting to modify the code from this repository to work with your own dataset: https://github.com/The-AI-Summer/simclr/blob/main/ai_summer_simclr_resnet18_stl10.py
You are trying to substitute the STL10 with your custom class, class ImageDataResourceDataset(VisionDataset):
def get_idr_dataloader(batch_size, transform=None, split="unlabeled"):
# idr = STL10("./", split=split, transform=transform, download=True)
idr = ImageDataResourceDataset(root=SOURCE_PATH, transform=Augment(224), split=split)
print(idr.data.shape, idr.labels.shape)
return DataLoader(dataset=idr, batch_size=batch_size, num_workers=cpu_count() // 2, ) # cpu_count() // 2
Therefore, the issue seems to be within the def __getitem__(self, idx): function under the ImageDataResourceDataset class.
def __getitem__(self, idx):
img = self.data[idx]
img = np.transpose(img, (1, 2, 0))
img = Image.fromarray(img)
img = self.transform(img)
return img
We compare it with the equivalent function in the original STL10 class from this repository: https://github.com/pytorch/vision/blob/main/torchvision/datasets/stl10.py#L102
def __getitem__(self, index: int) -> Tuple[Any, Any]:
"""
Args:
index (int): Index
Returns:
tuple: (image, target) where target is index of the target class.
"""
target: Optional[int]
if self.labels is not None:
img, target = self.data[index], int(self.labels[index])
else:
img, target = self.data[index], None
# doing this so that it is consistent with all other datasets
# to return a PIL Image
img = Image.fromarray(np.transpose(img, (1, 2, 0)))
if self.transform is not None:
img = self.transform(img)
if self.target_transform is not None:
target = self.target_transform(target)
return img, target
The __getitem__ function loads and returns a sample from the dataset at the specified index. However, it appears that you have omitted returning the target value in your custom function. Therefore, you should make sure to include the target in the return statement.
Answered By - Chih-Hao Liu
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