AxisError: axis 2 is out of bounds for array of dimension 0

[lsch0lz]

I' currently facing a strange behaviour when using GradCam for my tuned model. When I Fine-tune it from scratch everything works fine, but when I do Feature Extraction I get the mentioned error.

My Script for the training:

print("PyTorch` Version: ",torch.__version__)
print("Torchvision Version: ",torchvision.__version__)

data_dir = "/content/bt_models/data/training/"

# Models to choose from [resnet, alexnet, vgg, squeezenet, densenet, inception]
model_name = "resnet"

# Number of classes in the dataset
num_classes = 2

# Batch size for training (change depending on how much memory you have)
batch_size = 8

# Number of epochs to train for
num_epochs = 5

# Flag for feature extracting. When False, we finetune the whole model,
#   when True we only update the reshaped layer params
feature_extract = True

def train_model(model, dataloaders, criterion, optimizer, num_epochs=25, is_inception=False):
    since = time.time()

    val_acc_history = []

    best_model_wts = copy.deepcopy(model.state_dict())
    best_acc = 0.0

    for epoch in range(num_epochs):
        print('Epoch {}/{}'.format(epoch, num_epochs - 1))
        print('-' * 10)

        # Each epoch has a training and validation phase
        for phase in ['train', 'val']:
            if phase == 'train':
                model.train()  # Set model to training mode
            else:
                model.eval()   # Set model to evaluate mode

            running_loss = 0.0
            running_corrects = 0

            # Iterate over data.
            for inputs, labels in dataloaders[phase]:
                inputs = inputs.to(device)
                labels = labels.to(device)

                # zero the parameter gradients
                optimizer.zero_grad()

                # forward
                # track history if only in train
                with torch.set_grad_enabled(phase == 'train'):
                    # Get model outputs and calculate loss
                    # Special case for inception because in training it has an auxiliary output. In train
                    #   mode we calculate the loss by summing the final output and the auxiliary output
                    #   but in testing we only consider the final output.
                    if is_inception and phase == 'train':
                        # From https://discuss.pytorch.org/t/how-to-optimize-inception-model-with-auxiliary-classifiers/7958
                        outputs, aux_outputs = model(inputs)
                        loss1 = criterion(outputs, labels)
                        loss2 = criterion(aux_outputs, labels)
                        loss = loss1 + 0.4*loss2
                    else:
                        outputs = model(inputs)
                        loss = criterion(outputs, labels)

                    _, preds = torch.max(outputs, 1)

                    # backward + optimize only if in training phase
                    if phase == 'train':
                        loss.backward()
                        optimizer.step()

                # statistics
                running_loss += loss.item() * inputs.size(0)
                running_corrects += torch.sum(preds == labels.data)

            epoch_loss = running_loss / len(dataloaders[phase].dataset)
            epoch_acc = running_corrects.double() / len(dataloaders[phase].dataset)

            print('{} Loss: {:.4f} Acc: {:.4f}'.format(phase, epoch_loss, epoch_acc))

            # deep copy the model
            if phase == 'val' and epoch_acc > best_acc:
                best_acc = epoch_acc
                best_model_wts = copy.deepcopy(model.state_dict())
            if phase == 'val':
                val_acc_history.append(epoch_acc)

        print()

    time_elapsed = time.time() - since
    print('Training complete in {:.0f}m {:.0f}s'.format(time_elapsed // 60, time_elapsed % 60))
    print('Best val Acc: {:4f}'.format(best_acc))

    # load best model weights
    model.load_state_dict(best_model_wts)
    return model, val_acc_history

def set_parameter_requires_grad(model, feature_extracting):
    if feature_extracting:
        for param in model.parameters():
            param.requires_grad = False

def initialize_model(model_name, num_classes, feature_extract, use_pretrained=True):
    # Initialize these variables which will be set in this if statement. Each of these
    #   variables is model specific.
    model_ft = None
    input_size = 0

    if model_name == "resnet":
        """ Resnet18
        """
        model_ft = models.resnet18(pretrained=use_pretrained)
        set_parameter_requires_grad(model_ft, feature_extract)
        num_ftrs = model_ft.fc.in_features
        model_ft.fc = nn.Linear(num_ftrs, num_classes)
        input_size = 224

    elif model_name == "alexnet":
        """ Alexnet
        """
        model_ft = models.alexnet(pretrained=use_pretrained)
        set_parameter_requires_grad(model_ft, feature_extract)
        num_ftrs = model_ft.classifier[6].in_features
        model_ft.classifier[6] = nn.Linear(num_ftrs,num_classes)
        input_size = 224

    elif model_name == "vgg":
        """ VGG11_bn
        """
        model_ft = models.vgg11_bn(pretrained=use_pretrained)
        set_parameter_requires_grad(model_ft, feature_extract)
        num_ftrs = model_ft.classifier[6].in_features
        model_ft.classifier[6] = nn.Linear(num_ftrs,num_classes)
        input_size = 224

    elif model_name == "squeezenet":
        """ Squeezenet
        """
        model_ft = models.squeezenet1_0(pretrained=use_pretrained)
        set_parameter_requires_grad(model_ft, feature_extract)
        model_ft.classifier[1] = nn.Conv2d(512, num_classes, kernel_size=(1,1), stride=(1,1))
        model_ft.num_classes = num_classes
        input_size = 224

    elif model_name == "densenet":
        """ Densenet
        """
        model_ft = models.densenet121(pretrained=use_pretrained)
        set_parameter_requires_grad(model_ft, feature_extract)
        num_ftrs = model_ft.classifier.in_features
        model_ft.classifier = nn.Linear(num_ftrs, num_classes)
        input_size = 224

    elif model_name == "inception":
        """ Inception v3
        Be careful, expects (299,299) sized images and has auxiliary output
        """
        model_ft = models.inception_v3(pretrained=use_pretrained)
        set_parameter_requires_grad(model_ft, feature_extract)
        # Handle the auxilary net
        num_ftrs = model_ft.AuxLogits.fc.in_features
        model_ft.AuxLogits.fc = nn.Linear(num_ftrs, num_classes)
        # Handle the primary net
        num_ftrs = model_ft.fc.in_features
        model_ft.fc = nn.Linear(num_ftrs,num_classes)
        input_size = 299

    else:
        print("Invalid model name, exiting...")
        exit()

    return model_ft, input_size

# Initialize the model for this run
model_ft, input_size = initialize_model(model_name, num_classes, feature_extract, use_pretrained=True)

# Print the model we just instantiated
print(model_ft)

data_transforms = {
    'train': transforms.Compose([
        transforms.RandomResizedCrop(input_size),
        transforms.RandomHorizontalFlip(),
        transforms.ToTensor(),
        transforms.Normalize([0.485, 0.456, 0.406], [0.229, 0.224, 0.225])
    ]),
    'val': transforms.Compose([
        transforms.Resize(input_size),
        transforms.CenterCrop(input_size),
        transforms.ToTensor(),
        transforms.Normalize([0.485, 0.456, 0.406], [0.229, 0.224, 0.225])
    ]),
}

print("Initializing Datasets and Dataloaders...")

# Create training and validation datasets
image_datasets = {x: datasets.ImageFolder(os.path.join(data_dir, x), data_transforms[x]) for x in ['train', 'val']}
# Create training and validation dataloaders
dataloaders_dict = {x: torch.utils.data.DataLoader(image_datasets[x], batch_size=batch_size, shuffle=True, num_workers=4) for x in ['train', 'val']}

# Detect if we have a GPU available
device = torch.device("cuda:0" if torch.cuda.is_available() else "cpu")

# Send the model to GPU
model_ft = model_ft.to(device)

# Gather the parameters to be optimized/updated in this run. If we are
#  finetuning we will be updating all parameters. However, if we are
#  doing feature extract method, we will only update the parameters
#  that we have just initialized, i.e. the parameters with requires_grad
#  is True.
params_to_update = model_ft.parameters()
print("Params to learn:")
if feature_extract:
    params_to_update = []
    for name,param in model_ft.named_parameters():
        if param.requires_grad == True:
            params_to_update.append(param)
            print("\t",name)
else:
    for name,param in model_ft.named_parameters():
        if param.requires_grad == True:
            print("\t",name)

# Observe that all parameters are being optimized
optimizer_ft = optim.SGD(params_to_update, lr=0.001, momentum=0.9)

# Setup the loss fxn
criterion = nn.CrossEntropyLoss()

# Train and evaluate
model_ft, hist = train_model(model_ft, dataloaders_dict, criterion, optimizer_ft, num_epochs=num_epochs, is_inception=(model_name=="inception"))

# Initialize the non-pretrained version of the model used for this run
scratch_model,_ = initialize_model(model_name, num_classes, feature_extract=False, use_pretrained=False)
scratch_model = scratch_model.to(device)
scratch_optimizer = optim.SGD(scratch_model.parameters(), lr=0.001, momentum=0.9)
scratch_criterion = nn.CrossEntropyLoss()
_,scratch_hist = train_model(scratch_model, dataloaders_dict, scratch_criterion, scratch_optimizer, num_epochs=num_epochs, is_inception=(model_name=="inception"))

# Plot the training curves of validation accuracy vs. number
#  of training epochs for the transfer learning method and
#  the model trained from scratch
ohist = []
shist = []

ohist = [h.cpu().numpy() for h in hist]
shist = [h.cpu().numpy() for h in scratch_hist]

plt.title("Validation Accuracy vs. Number of Training Epochs")
plt.xlabel("Training Epochs")
plt.ylabel("Validation Accuracy")
plt.plot(range(1,num_epochs+1),ohist,label="Pretrained")
plt.plot(range(1,num_epochs+1),shist,label="Scratch")
plt.ylim((0,1.))
plt.xticks(np.arange(1, num_epochs+1, 1.0))
plt.legend()
plt.show()

The GradCam Script which works for Fine-tuned models:

from PIL import Image
from pytorch_grad_cam import GradCAM, ScoreCAM, GradCAMPlusPlus, AblationCAM, XGradCAM, EigenCAM, FullGrad
from pytorch_grad_cam.utils.model_targets import ClassifierOutputTarget
from pytorch_grad_cam.utils.image import show_cam_on_image, preprocess_image
from torchvision.models import resnet50
transform = torchvision.transforms.Compose([
    torchvision.transforms.ToTensor(),
])
# model = resnet50(pretrained=True)
model = model_ft
#model = resnet50(pretrained=True)
target_layers = [model.layer4[-1]]

# rgb_img = cv2.imread("/content/bt_models/data/training/val/doctor/images (1).jpg")
rgb_img = Image.open('/content/bt_models/data/training/val/doctor/images (1).jpg')
print(type(rgb_img))
rgb_img = np.float32(rgb_img) / 255
input_tensor = preprocess_image(rgb_img, mean=[0.485, 0.456, 0.406], std=[0.229, 0.224, 0.225])

# Create an input tensor image for your model..
# Note: input_tensor can be a batch tensor with several images!

# Construct the CAM object once, and then re-use it on many images:
cam = GradCAM(model=model, target_layers=target_layers, use_cuda=True)
print(cam)

# You can also use it within a with statement, to make sure it is freed,
# In case you need to re-create it inside an outer loop:
# with GradCAM(model=model, target_layers=target_layers, use_cuda=args.use_cuda) as cam:
#   ...

# We have to specify the target we want to generate
# the Class Activation Maps for.
# If targets is None, the highest scoring category
# will be used for every image in the batch.
# Here we use ClassifierOutputTarget, but you can define your own custom targets
# That are, for example, combinations of categories, or specific outputs in a non standard model.
targets = [ClassifierOutputTarget(281)]

# You can also pass aug_smooth=True and eigen_smooth=True, to apply smoothing.
grayscale_cam = cam(input_tensor=input_tensor)

# In this example grayscale_cam has only one image in the batch:
grayscale_cam = grayscale_cam[0, :]
visualization = show_cam_on_image(rgb_img, grayscale_cam, use_rgb=True)

Any ideas where the problem could be?

[jacobgil]

Hi, what is the line that crashes ? Can you paste a code snippet of the actual code that crashes ? Is the crash when using gradcam or when doing something else ?

[lsch0lz]

Hi! It crashes when using the cam object:

AxisError                                 Traceback (most recent call last)
[<ipython-input-7-db02c72a6749>](https://vl7u1jefvqc-496ff2e9c6d22116-0-colab.googleusercontent.com/outputframe.html?vrz=colab-20220518-060055-RC00_449411064#) in <module>()
     40 
     41 # You can also pass aug_smooth=True and eigen_smooth=True, to apply smoothing.
---> 42 grayscale_cam = cam(input_tensor=input_tensor)
     43 
     44 # In this example grayscale_cam has only one image in the batch:

7 frames
<__array_function__ internals> in mean(*args, **kwargs)

[/usr/local/lib/python3.7/dist-packages/numpy/core/_methods.py](https://vl7u1jefvqc-496ff2e9c6d22116-0-colab.googleusercontent.com/outputframe.html?vrz=colab-20220518-060055-RC00_449411064#) in _count_reduce_items(arr, axis, keepdims, where)
     74         items = nt.intp(1)
     75         for ax in axis:
---> 76             items *= arr.shape[mu.normalize_axis_index(ax, arr.ndim)]
     77     else:
     78         # TODO: Optimize case when `where` is broadcast along a non-reduction

AxisError: axis 2 is out of bounds for array of dimension 0

The input_tensor is torch.Size([1, 3, 100, 100])

[jacobgil]

Thanks. What is the definition of this feature extraction network that makes it crash, and of the target_layer ? The output of the feature extraction network is still the number of categories, right ?

[lsch0lz]

@jacobgil The last Layer is defined as: model_ft.fc = nn.Linear(num_ftrs, num_classes) num_classes is 2, because I want to classify the classs 'doctor' and 'nurse'. So yes, the output is the number of categories.

eval() gives me the following structure:

ResNet(
  (conv1): Conv2d(3, 64, kernel_size=(7, 7), stride=(2, 2), padding=(3, 3), bias=False)
  (bn1): BatchNorm2d(64, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
  (relu): ReLU(inplace=True)
  (maxpool): MaxPool2d(kernel_size=3, stride=2, padding=1, dilation=1, ceil_mode=False)
  (layer1): Sequential(
    (0): BasicBlock(
      (conv1): Conv2d(64, 64, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1), bias=False)
      (bn1): BatchNorm2d(64, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
      (relu): ReLU(inplace=True)
      (conv2): Conv2d(64, 64, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1), bias=False)
      (bn2): BatchNorm2d(64, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
    )
    (1): BasicBlock(
      (conv1): Conv2d(64, 64, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1), bias=False)
      (bn1): BatchNorm2d(64, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
      (relu): ReLU(inplace=True)
      (conv2): Conv2d(64, 64, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1), bias=False)
      (bn2): BatchNorm2d(64, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
    )
  )
  (layer2): Sequential(
    (0): BasicBlock(
      (conv1): Conv2d(64, 128, kernel_size=(3, 3), stride=(2, 2), padding=(1, 1), bias=False)
      (bn1): BatchNorm2d(128, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
      (relu): ReLU(inplace=True)
      (conv2): Conv2d(128, 128, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1), bias=False)
      (bn2): BatchNorm2d(128, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
      (downsample): Sequential(
        (0): Conv2d(64, 128, kernel_size=(1, 1), stride=(2, 2), bias=False)
        (1): BatchNorm2d(128, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
      )
    )
    (1): BasicBlock(
      (conv1): Conv2d(128, 128, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1), bias=False)
      (bn1): BatchNorm2d(128, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
      (relu): ReLU(inplace=True)
      (conv2): Conv2d(128, 128, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1), bias=False)
      (bn2): BatchNorm2d(128, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
    )
  )
  (layer3): Sequential(
    (0): BasicBlock(
      (conv1): Conv2d(128, 256, kernel_size=(3, 3), stride=(2, 2), padding=(1, 1), bias=False)
      (bn1): BatchNorm2d(256, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
      (relu): ReLU(inplace=True)
      (conv2): Conv2d(256, 256, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1), bias=False)
      (bn2): BatchNorm2d(256, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
      (downsample): Sequential(
        (0): Conv2d(128, 256, kernel_size=(1, 1), stride=(2, 2), bias=False)
        (1): BatchNorm2d(256, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
      )
    )
    (1): BasicBlock(
      (conv1): Conv2d(256, 256, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1), bias=False)
      (bn1): BatchNorm2d(256, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
      (relu): ReLU(inplace=True)
      (conv2): Conv2d(256, 256, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1), bias=False)
      (bn2): BatchNorm2d(256, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
    )
  )
  (layer4): Sequential(
    (0): BasicBlock(
      (conv1): Conv2d(256, 512, kernel_size=(3, 3), stride=(2, 2), padding=(1, 1), bias=False)
      (bn1): BatchNorm2d(512, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
      (relu): ReLU(inplace=True)
      (conv2): Conv2d(512, 512, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1), bias=False)
      (bn2): BatchNorm2d(512, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
      (downsample): Sequential(
        (0): Conv2d(256, 512, kernel_size=(1, 1), stride=(2, 2), bias=False)
        (1): BatchNorm2d(512, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
      )
    )
    (1): BasicBlock(
      (conv1): Conv2d(512, 512, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1), bias=False)
      (bn1): BatchNorm2d(512, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
      (relu): ReLU(inplace=True)
      (conv2): Conv2d(512, 512, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1), bias=False)
      (bn2): BatchNorm2d(512, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
    )
  )
  (avgpool): AdaptiveAvgPool2d(output_size=(1, 1))
  (fc): Linear(in_features=512, out_features=2, bias=True)
)

Does that information helps?

[jacobgil]

Yes but I'm still missing some context, sorry. What is the difference in the model/setting when it works and when it crashes ?

[lsch0lz]

@jacobgil no worries! I'm glad you are helping. So if feature_extract is true the model only learns the weights for the parameters that don't require gradients. As far as I understand this tutorial Fine tune PyTorch Model only the last layer is changed because of this. When I compare the structure between feature_extract True and False it seems the same. But GradCam only works when feature_extract is false. I could image that the change of the last layer is messing something up, but I'm not sure tbh Maybe I'm missing something here...

[jacobgil]

Oh now I get it. It might be possible that since the require grads is false for that model, grad-cam isn't able to compute the gradients for it. Can you try turning on requires_grad for the target layer in the model before calling the cam object (and then if you need to, turn it off when it's finished) ?

[lsch0lz]

Makes sense. Do you mean turning on requires_grad like this:

model.layer4[-1].requires_grad = True
target_layers = [model.layer4[-1]]

This still gives me the following error:

AxisError                                 Traceback (most recent call last)
[<ipython-input-8-72acee2d8440>](https://vl7u1jefvqc-496ff2e9c6d22116-0-colab.googleusercontent.com/outputframe.html?vrz=colab-20220518-060055-RC00_449411064#) in <module>()
     42 
     43 # You can also pass aug_smooth=True and eigen_smooth=True, to apply smoothing.
---> 44 grayscale_cam = cam(input_tensor=input_tensor)
     45 
     46 # In this example grayscale_cam has only one image in the batch:

7 frames
<__array_function__ internals> in mean(*args, **kwargs)

[/usr/local/lib/python3.7/dist-packages/numpy/core/_methods.py](https://vl7u1jefvqc-496ff2e9c6d22116-0-colab.googleusercontent.com/outputframe.html?vrz=colab-20220518-060055-RC00_449411064#) in _count_reduce_items(arr, axis, keepdims, where)
     74         items = nt.intp(1)
     75         for ax in axis:
---> 76             items *= arr.shape[mu.normalize_axis_index(ax, arr.ndim)]
     77     else:
     78         # TODO: Optimize case when `where` is broadcast along a non-reduction

AxisError: axis 2 is out of bounds for array of dimension 0

The target_layers is:

[BasicBlock(
  (conv1): Conv2d(512, 512, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1), bias=False)
  (bn1): BatchNorm2d(512, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
  (relu): ReLU(inplace=True)
  (conv2): Conv2d(512, 512, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1), bias=False)
  (bn2): BatchNorm2d(512, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
)]

[jacobgil]

Can you please try looping over all the layers and setting requires grad before calling CAM?

for param in model.parameters():
        param.requires_grad = False

If this works, then I think you probably want to return the model back to it's previous state (e.g if you are using this inside the training loop).

Then something like this could work in total:

Before calling the cam:

params_with_requires_grad = []
for param in model.parameters():
    if param.requires_grad:
        param.requires_grad = False
        params_with_requires_grad.append(param)

Then reverting the model state back after calling cam:

for param in params_with_requires_grad:
    param.requires_grad=True

Does this work ?

[lsch0lz]

Calling:

for param in model.parameters():
        param.requires_grad = False

before the cam doesn't work, but when I set param.requires_grad = True it works. So if I understand this correctly thee actual state of the model is more important than how I trained the model. Thanks a lot @jacobgil! Have a nice Sunday