fastai imports are deprecated

[Tato14]

With the new stable version when:

from fastai2_extensions.interpret.all import *

it throws an error:

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
<ipython-input-345-5bb73445d9e5> in <module>
----> 1 from fastai2_extensions.interpret.all import *

~/anaconda3/envs/fastai2/lib/python3.8/site-packages/fastai2_extensions/interpret/all.py in <module>
----> 1 from .compare import *
      2 from .gradcam import *
      3 from .interpret import *

~/anaconda3/envs/fastai2/lib/python3.8/site-packages/fastai2_extensions/interpret/compare.py in <module>
      4 
      5 # Cell
----> 6 from fastai2.vision.all import *
      7 from . import *
      8 

ModuleNotFoundError: No module named 'fastai2'

[Tato14]

Also, Tuple should be renamed to fastuple

[willjobs]

To expand on this, there are issues with the current stable version of fastai v2. For example, this bit of code from the README in the amalgam repo no longer works:

interp = ClassificationInterpretationEx.from_learner(learn)

It throws this error:

TypeError: __init__() missing 1 required positional argument: 'losses'

[rsomani95]

Hey, sorry I seemed to have missed this issue.

We've changed the package name to fastai-amalgam, and the README didn't reflect that. Can you try pip install fastai-amalgam and see if the error persists?

[rsomani95]

You'll also need to change the bits of your code that go from fastai2_extensions... to from fastai_amalgam...

[willjobs]

Thanks, @rsomani95! I tried that, and I'm still getting the same error as above. I'm using Google Colab (no GPU) with:

• fastai==2.2.5
• fastcore==1.3.19
• fastai-amalgam==0.0.26
• torch==1.7.0+cu101
• torchvision==0.8.1+cu101

My model is a cnn_learner built off resnet50.

[rsomani95]

@willjobs Can you try using the regular fastai ClassificationInterpretation class?
The part that's failing is happening from the base fastai class.

Does your Learner have a loss_func attached?

[willjobs]

I just tried replicating what you did in the interpret_gradcam.ipynb notebook, and I get all the way down to plot_gcam() which throws the error: "RuntimeError: number of dims don't match in permute".

[willjobs]

@willjobs Can you try using the regular fastai ClassificationInterpretation class?
The part that's failing is happening from the base fastai class.

Does your Learner have a loss_func attached?

Yup, I just tried it and got the same error with ClassificationInterpretation. When I evaluate learn.loss_func, I get FlattenedLoss of CrossEntropyLoss().

[rsomani95]

I just tried replicating what you did in the interpret_gradcam.ipynb notebook, and I get all the way down to plot_gcam() which throws the error: "RuntimeError: number of dims don't match in permute".

Ah, that's actually deprecated, I re-implemented a different interface using the same underlying components. Try Learner.gradcam(...); it moves away from matplotlib and uses PIL for all the plotting

[rsomani95]

@willjobs Can you try using the regular fastai ClassificationInterpretation class?
The part that's failing is happening from the base fastai class.
Does your Learner have a loss_func attached?

Yup, I just tried it and got the same error with ClassificationInterpretation. When I evaluate learn.loss_func, I get FlattenedLoss of CrossEntropyLoss().

This is odd. It's something on the fastai side of things, and so I'm not sure I can fix it. I'll try re-running some tests with the latest version, but it'd be best to ask on the fastai forums

[willjobs]

Ah, that's actually deprecated, I re-implemented a different interface using the same underlying components. Try Learner.gradcam(...); it moves away from matplotlib and uses PIL for all the plotting

Gotcha. I just tried this (learn.gradcam) and got the same error :(

This is odd. It's something on the fastai side of things, and so I'm not sure I can fix it. I'll try re-running some tests with the latest version, but it'd be best to ask on the fastai forums

OK, will do. I wonder if the issue is that I'm using a ResNet? It has adaptive pooling and two Linear layers after the last convolutional layer, and I'm not sure exactly how that works with gradcam. The network I'm using has this structure:

Sequential(
(0): Sequential(
    (0): Conv2d(3, 64, kernel_size=(7, 7), stride=(2, 2), padding=(3, 3), bias=False)
    (1): BatchNorm2d(64, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
    (2): ReLU(inplace=True)
    (3): MaxPool2d(kernel_size=3, stride=2, padding=1, dilation=1, ceil_mode=False)
    (4): Sequential(
    (0): Bottleneck(
        (conv1): Conv2d(64, 64, kernel_size=(1, 1), stride=(1, 1), bias=False)
        (bn1): BatchNorm2d(64, eps=1e-05, momentum=0.1, affine=True, track_running_stats=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)
        (conv3): Conv2d(64, 256, kernel_size=(1, 1), stride=(1, 1), bias=False)
        (bn3): BatchNorm2d(256, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
        (relu): ReLU(inplace=True)
        (downsample): Sequential(
        (0): Conv2d(64, 256, kernel_size=(1, 1), stride=(1, 1), bias=False)
        (1): BatchNorm2d(256, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
        )
    )
    (1): Bottleneck(
        (conv1): Conv2d(256, 64, kernel_size=(1, 1), stride=(1, 1), bias=False)
        (bn1): BatchNorm2d(64, eps=1e-05, momentum=0.1, affine=True, track_running_stats=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)
        (conv3): Conv2d(64, 256, kernel_size=(1, 1), stride=(1, 1), bias=False)
        (bn3): BatchNorm2d(256, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
        (relu): ReLU(inplace=True)
    )
    (2): Bottleneck(
        (conv1): Conv2d(256, 64, kernel_size=(1, 1), stride=(1, 1), bias=False)
        (bn1): BatchNorm2d(64, eps=1e-05, momentum=0.1, affine=True, track_running_stats=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)
        (conv3): Conv2d(64, 256, kernel_size=(1, 1), stride=(1, 1), bias=False)
        (bn3): BatchNorm2d(256, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
        (relu): ReLU(inplace=True)
    )
    )
    (5): Sequential(
    (0): Bottleneck(
        (conv1): Conv2d(256, 128, kernel_size=(1, 1), stride=(1, 1), bias=False)
        (bn1): BatchNorm2d(128, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
        (conv2): Conv2d(128, 128, kernel_size=(3, 3), stride=(2, 2), padding=(1, 1), bias=False)
        (bn2): BatchNorm2d(128, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
        (conv3): Conv2d(128, 512, kernel_size=(1, 1), stride=(1, 1), bias=False)
        (bn3): BatchNorm2d(512, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
        (relu): ReLU(inplace=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): Bottleneck(
        (conv1): Conv2d(512, 128, kernel_size=(1, 1), stride=(1, 1), bias=False)
        (bn1): BatchNorm2d(128, eps=1e-05, momentum=0.1, affine=True, track_running_stats=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)
        (conv3): Conv2d(128, 512, kernel_size=(1, 1), stride=(1, 1), bias=False)
        (bn3): BatchNorm2d(512, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
        (relu): ReLU(inplace=True)
    )
    (2): Bottleneck(
        (conv1): Conv2d(512, 128, kernel_size=(1, 1), stride=(1, 1), bias=False)
        (bn1): BatchNorm2d(128, eps=1e-05, momentum=0.1, affine=True, track_running_stats=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)
        (conv3): Conv2d(128, 512, kernel_size=(1, 1), stride=(1, 1), bias=False)
        (bn3): BatchNorm2d(512, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
        (relu): ReLU(inplace=True)
    )
    (3): Bottleneck(
        (conv1): Conv2d(512, 128, kernel_size=(1, 1), stride=(1, 1), bias=False)
        (bn1): BatchNorm2d(128, eps=1e-05, momentum=0.1, affine=True, track_running_stats=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)
        (conv3): Conv2d(128, 512, kernel_size=(1, 1), stride=(1, 1), bias=False)
        (bn3): BatchNorm2d(512, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
        (relu): ReLU(inplace=True)
    )
    )
    (6): Sequential(
    (0): Bottleneck(
        (conv1): Conv2d(512, 256, kernel_size=(1, 1), stride=(1, 1), bias=False)
        (bn1): BatchNorm2d(256, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
        (conv2): Conv2d(256, 256, kernel_size=(3, 3), stride=(2, 2), padding=(1, 1), bias=False)
        (bn2): BatchNorm2d(256, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
        (conv3): Conv2d(256, 1024, kernel_size=(1, 1), stride=(1, 1), bias=False)
        (bn3): BatchNorm2d(1024, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
        (relu): ReLU(inplace=True)
        (downsample): Sequential(
        (0): Conv2d(512, 1024, kernel_size=(1, 1), stride=(2, 2), bias=False)
        (1): BatchNorm2d(1024, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
        )
    )
    (1): Bottleneck(
        (conv1): Conv2d(1024, 256, kernel_size=(1, 1), stride=(1, 1), bias=False)
        (bn1): BatchNorm2d(256, eps=1e-05, momentum=0.1, affine=True, track_running_stats=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)
        (conv3): Conv2d(256, 1024, kernel_size=(1, 1), stride=(1, 1), bias=False)
        (bn3): BatchNorm2d(1024, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
        (relu): ReLU(inplace=True)
    )
    (2): Bottleneck(
        (conv1): Conv2d(1024, 256, kernel_size=(1, 1), stride=(1, 1), bias=False)
        (bn1): BatchNorm2d(256, eps=1e-05, momentum=0.1, affine=True, track_running_stats=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)
        (conv3): Conv2d(256, 1024, kernel_size=(1, 1), stride=(1, 1), bias=False)
        (bn3): BatchNorm2d(1024, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
        (relu): ReLU(inplace=True)
    )
    (3): Bottleneck(
        (conv1): Conv2d(1024, 256, kernel_size=(1, 1), stride=(1, 1), bias=False)
        (bn1): BatchNorm2d(256, eps=1e-05, momentum=0.1, affine=True, track_running_stats=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)
        (conv3): Conv2d(256, 1024, kernel_size=(1, 1), stride=(1, 1), bias=False)
        (bn3): BatchNorm2d(1024, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
        (relu): ReLU(inplace=True)
    )
    (4): Bottleneck(
        (conv1): Conv2d(1024, 256, kernel_size=(1, 1), stride=(1, 1), bias=False)
        (bn1): BatchNorm2d(256, eps=1e-05, momentum=0.1, affine=True, track_running_stats=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)
        (conv3): Conv2d(256, 1024, kernel_size=(1, 1), stride=(1, 1), bias=False)
        (bn3): BatchNorm2d(1024, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
        (relu): ReLU(inplace=True)
    )
    (5): Bottleneck(
        (conv1): Conv2d(1024, 256, kernel_size=(1, 1), stride=(1, 1), bias=False)
        (bn1): BatchNorm2d(256, eps=1e-05, momentum=0.1, affine=True, track_running_stats=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)
        (conv3): Conv2d(256, 1024, kernel_size=(1, 1), stride=(1, 1), bias=False)
        (bn3): BatchNorm2d(1024, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
        (relu): ReLU(inplace=True)
    )
    )
    (7): Sequential(
    (0): Bottleneck(
        (conv1): Conv2d(1024, 512, kernel_size=(1, 1), stride=(1, 1), bias=False)
        (bn1): BatchNorm2d(512, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
        (conv2): Conv2d(512, 512, kernel_size=(3, 3), stride=(2, 2), padding=(1, 1), bias=False)
        (bn2): BatchNorm2d(512, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
        (conv3): Conv2d(512, 2048, kernel_size=(1, 1), stride=(1, 1), bias=False)
        (bn3): BatchNorm2d(2048, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
        (relu): ReLU(inplace=True)
        (downsample): Sequential(
        (0): Conv2d(1024, 2048, kernel_size=(1, 1), stride=(2, 2), bias=False)
        (1): BatchNorm2d(2048, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
        )
    )
    (1): Bottleneck(
        (conv1): Conv2d(2048, 512, kernel_size=(1, 1), stride=(1, 1), bias=False)
        (bn1): BatchNorm2d(512, eps=1e-05, momentum=0.1, affine=True, track_running_stats=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)
        (conv3): Conv2d(512, 2048, kernel_size=(1, 1), stride=(1, 1), bias=False)
        (bn3): BatchNorm2d(2048, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
        (relu): ReLU(inplace=True)
    )
    (2): Bottleneck(
        (conv1): Conv2d(2048, 512, kernel_size=(1, 1), stride=(1, 1), bias=False)
        (bn1): BatchNorm2d(512, eps=1e-05, momentum=0.1, affine=True, track_running_stats=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)
        (conv3): Conv2d(512, 2048, kernel_size=(1, 1), stride=(1, 1), bias=False)
        (bn3): BatchNorm2d(2048, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
        (relu): ReLU(inplace=True)
    )
    )
)
(1): Sequential(
    (0): AdaptiveConcatPool2d(
    (ap): AdaptiveAvgPool2d(output_size=1)
    (mp): AdaptiveMaxPool2d(output_size=1)
    )
    (1): Flatten(full=False)
    (2): BatchNorm1d(4096, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
    (3): Dropout(p=0.25, inplace=False)
    (4): Linear(in_features=4096, out_features=512, bias=False)
    (5): ReLU(inplace=True)
    (6): BatchNorm1d(512, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
    (7): Dropout(p=0.5, inplace=False)
    (8): Linear(in_features=512, out_features=150, bias=False)
)
) 

[rsomani95]

I wonder if the issue is that I'm using a ResNet?

This may be what's causing the error in Learner.gradcam. I haven't tested it with a ResNet-50, but it should work if you specify the exact output layer with respect to which you want the gradcam output for to the target_layer param. From the network structure you printed above, something like this may work:

learn = cnn_learner(...)
learn.gradcam(..., target_layer = learn.model[1][0])

I'd tinker with the target_layer param, you could try learn.model[0][0] to get a heatmap w.r.t the first conv layer for a sanity check

[willjobs]

I'd tinker with the target_layer param, you could try learn.model[0][0] to get a heatmap w.r.t the first conv layer for a sanity check

Good idea. It works with learn.model[0][0], so that's good. It doesn't work with learn.model[1][0], unfortunately (I get the same "number of dims don't match in permute" error) .

I also tried learn.model[1][4] (the first linear layer) and learn.model[1][8] (the last linear layer/target layer) and neither works (I get a "Dimension out of range" error). I wonder if it's because of the Flatten layer?

Also, thank you for all your help on this! I really appreciate it.

[rsomani95]

Ahhh, that's weird. I'll have to take a deeper look at this to figure out what the issue is. I've only tested this with a mobilenet-v2. This is a good issue to solve though. Could you create a dedicated issue for this separately so we can track it? Thanks.

Also, thank you for all your help on this! I really appreciate it.
No prob!

[willjobs]

Will do!