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thtang / CheXNet-with-localization

Weakly Supervised Learning for Findings Detection in Medical Images
https://www.csie.ntu.edu.tw/~yvchen/f106-adl/doc/HTCMedical.pdf
GNU General Public License v3.0
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Invalid layer name: module.densenet121.features.denseblock4.denselayer16.conv.2 #8

Open rajdeinno opened 5 years ago

rajdeinno commented 5 years ago

Hi,

I got the below error while running denseNet_localization.py file. 

Traceback (most recent call last):
  File "/media/administrator/D/XRay/CheXnet_Demo/denseNet_localization.py", line 227, in <module>
    output = gcam.generate(target_layer="module.densenet121.features.denseblock4.denselayer16.conv.2")
  File "/media/administrator/D/XRay/CheXnet_Demo/denseNet_localization.py", line 186, in generate
    fmaps = self._find(self.all_fmaps, target_layer)
  File "/media/administrator/D/XRay/CheXnet_Demo/denseNet_localization.py", line 174, in _find
    raise ValueError('Invalid layer name: {}'.format(target_layer))
ValueError: Invalid layer name: module.densenet121.features.denseblock4.denselayer16.conv.2

any help would be really appriciated.. Thanks in advance..

thtang commented 5 years ago

Do you use Pytorch==0.2.0 and torchvision==0.2.0 ?

rajdeinno commented 5 years ago

I am using the below version since I had some problem with torchvision 0.2.0.

torch==1.1.0 torchvision==0.2.2

Additional info: I ran my training by using the below requirements in Ubuntu 16.04.

python== 3.5.6 pip 19.1.1 pkg-resources 0.0.0
setuptools 41.0.1 wheel 0.33.4

cycler==0.10.0 decorator==4.4.0 imageio==2.5.0 joblib==0.13.2 matplotlib==2.1.1 networkx==2.3 numpy==1.13.3 opencv-python==3.4.0.12 pandas==0.24.2 Pillow==6.0.0 pyparsing==2.4.0 python-dateutil==2.8.0 pytz==2019.1 PyWavelets==1.0.3 scikit-image==0.13.1 scikit-learn==0.21.1 scipy==1.0.0 six==1.12.0 torch==1.1.0 torchvision==0.2.2

rajdeinno commented 5 years ago

If I use torchvision 0.2.0 and torch==1.0.1 I get the following error.

warn("The default mode, 'constant', will be changed to 'reflect' in "
0
Traceback (most recent call last):
  File "denseNet_localization.py", line 76, in <module>
    model = DenseNet121(8).cuda()
  File "denseNet_localization.py", line 65, in __init__
    self.densenet121 = torchvision.models.densenet121(pretrained=True)
  File "/home/administrator/Desktop/Projects/xray/chexnet/setup3.5/lib/python3.5/site-packages/torchvision/models/densenet.py", line 26, in densenet121
    **kwargs)
  File "/home/administrator/Desktop/Projects/xray/chexnet/setup3.5/lib/python3.5/site-packages/torchvision/models/densenet.py", line 142, in __init__
    bn_size=bn_size, growth_rate=growth_rate, drop_rate=drop_rate)
  File "/home/administrator/Desktop/Projects/xray/chexnet/setup3.5/lib/python3.5/site-packages/torchvision/models/densenet.py", line 98, in __init__
    layer = _DenseLayer(num_input_features + i * growth_rate, growth_rate, bn_size, drop_rate)
  File "/home/administrator/Desktop/Projects/xray/chexnet/setup3.5/lib/python3.5/site-packages/torchvision/models/densenet.py", line 77, in __init__
    self.add_module('norm.1', nn.BatchNorm2d(num_input_features)),
  File "/home/administrator/Desktop/Projects/xray/chexnet/setup3.5/lib/python3.5/site-packages/torch/nn/modules/module.py", line 180, in add_module
    raise KeyError("module name can't contain \".\"")
KeyError: 'module name can\'t contain "."'

So I have upgraded torchvision to 0.2.2. and torch==1.1.0. and my train went successful. When I try to run denseNet_localization.py file then I got the above error.

thtang commented 5 years ago

Ok, so it seems that the errors are just caused by the different version of packages.

rajdeinno commented 5 years ago

It worked for me after I changed the name in denseNet_localization.py module.densenet121.features.denseblock4.denselayer16.conv.2 to module.densenet121.features.denseblock4.denselayer16.conv2

And I had some package version issues as well.

rajdeinno commented 5 years ago

Hi Tang,

I am able to generate the bound_box.txt file after I execute the denseNet_localization.pyfile. how to visualize the bound box text file into the input image? as you mentioned in ground-truth label (red) and its prediction (blue). Thanks in advance..

Please assist me on this..

Sent from my iPhone

On 28-May-2019, at 17:57, T.H. Tang notifications@github.com wrote:

It seem that the errors are just caused by the different version of packages.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

mochita314 commented 4 years ago

I changed module.densenet121.features.denseblock4.denselayer16.conv.2 to module.densenet121.features.denseblock4.denselayer16.conv2 but still have same problem. What should I do ... ??

I'm using torch (1.0.1.post2) torchvision (0.2.2.post3)


  File "denseNet_localization.py", line 247, in <module>
    output = gcam.generate(target_layer="module.densenet121.features.denseblock4.denselayer16.conv2")
  File "denseNet_localization.py", line 211, in generate
    fmaps = self._find(self.all_fmaps, target_layer)
  File "denseNet_localization.py", line 199, in _find
    raise ValueError('Invalid layer name: {}'.format(target_layer))
ValueError: Invalid layer name: module.densenet121.features.denseblock4.denselayer16.conv2```
sp7414 commented 3 years ago

I changed module.densenet121.features.denseblock4.denselayer16.conv.2 to module.densenet121.features.denseblock4.denselayer16.conv2 but still have same problem. What should I do ... ??

I'm using torch (1.0.1.post2) torchvision (0.2.2.post3)

  File "denseNet_localization.py", line 247, in <module>
    output = gcam.generate(target_layer="module.densenet121.features.denseblock4.denselayer16.conv2")
  File "denseNet_localization.py", line 211, in generate
    fmaps = self._find(self.all_fmaps, target_layer)
  File "denseNet_localization.py", line 199, in _find
    raise ValueError('Invalid layer name: {}'.format(target_layer))
ValueError: Invalid layer name: module.densenet121.features.denseblock4.denselayer16.conv2```

have you solved this problem? I'm facing the same issue.

ankitdata commented 3 years ago

I changed module.densenet121.features.denseblock4.denselayer16.conv.2 to module.densenet121.features.denseblock4.denselayer16.conv2 but still have same problem. What should I do ... ?? I'm using torch (1.0.1.post2) torchvision (0.2.2.post3)

  File "denseNet_localization.py", line 247, in <module>
    output = gcam.generate(target_layer="module.densenet121.features.denseblock4.denselayer16.conv2")
  File "denseNet_localization.py", line 211, in generate
    fmaps = self._find(self.all_fmaps, target_layer)
  File "denseNet_localization.py", line 199, in _find
    raise ValueError('Invalid layer name: {}'.format(target_layer))
ValueError: Invalid layer name: module.densenet121.features.denseblock4.denselayer16.conv2```

have you solved this problem? I'm facing the same issue.

see this issue might helpfull

Aliktk commented 3 years ago

If I use torchvision 0.2.0 and torch==1.0.1 I get the following error.

warn("The default mode, 'constant', will be changed to 'reflect' in "
0
Traceback (most recent call last):
  File "denseNet_localization.py", line 76, in <module>
    model = DenseNet121(8).cuda()
  File "denseNet_localization.py", line 65, in __init__
    self.densenet121 = torchvision.models.densenet121(pretrained=True)
  File "/home/administrator/Desktop/Projects/xray/chexnet/setup3.5/lib/python3.5/site-packages/torchvision/models/densenet.py", line 26, in densenet121
    **kwargs)
  File "/home/administrator/Desktop/Projects/xray/chexnet/setup3.5/lib/python3.5/site-packages/torchvision/models/densenet.py", line 142, in __init__
    bn_size=bn_size, growth_rate=growth_rate, drop_rate=drop_rate)
  File "/home/administrator/Desktop/Projects/xray/chexnet/setup3.5/lib/python3.5/site-packages/torchvision/models/densenet.py", line 98, in __init__
    layer = _DenseLayer(num_input_features + i * growth_rate, growth_rate, bn_size, drop_rate)
  File "/home/administrator/Desktop/Projects/xray/chexnet/setup3.5/lib/python3.5/site-packages/torchvision/models/densenet.py", line 77, in __init__
    self.add_module('norm.1', nn.BatchNorm2d(num_input_features)),
  File "/home/administrator/Desktop/Projects/xray/chexnet/setup3.5/lib/python3.5/site-packages/torch/nn/modules/module.py", line 180, in add_module
    raise KeyError("module name can't contain \".\"")
KeyError: 'module name can\'t contain "."'

So I have upgraded torchvision to 0.2.2. and torch==1.1.0. and my train went successful. When I try to run denseNet_localization.py file then I got the above error.

Hello @rajdeinno how did u solve this error please healp me in this regard. Thanks @rajdeinno

ankitdata commented 3 years ago

If I use torchvision 0.2.0 and torch==1.0.1 I get the following error.

warn("The default mode, 'constant', will be changed to 'reflect' in "
0
Traceback (most recent call last):
  File "denseNet_localization.py", line 76, in <module>
    model = DenseNet121(8).cuda()
  File "denseNet_localization.py", line 65, in __init__
    self.densenet121 = torchvision.models.densenet121(pretrained=True)
  File "/home/administrator/Desktop/Projects/xray/chexnet/setup3.5/lib/python3.5/site-packages/torchvision/models/densenet.py", line 26, in densenet121
    **kwargs)
  File "/home/administrator/Desktop/Projects/xray/chexnet/setup3.5/lib/python3.5/site-packages/torchvision/models/densenet.py", line 142, in __init__
    bn_size=bn_size, growth_rate=growth_rate, drop_rate=drop_rate)
  File "/home/administrator/Desktop/Projects/xray/chexnet/setup3.5/lib/python3.5/site-packages/torchvision/models/densenet.py", line 98, in __init__
    layer = _DenseLayer(num_input_features + i * growth_rate, growth_rate, bn_size, drop_rate)
  File "/home/administrator/Desktop/Projects/xray/chexnet/setup3.5/lib/python3.5/site-packages/torchvision/models/densenet.py", line 77, in __init__
    self.add_module('norm.1', nn.BatchNorm2d(num_input_features)),
  File "/home/administrator/Desktop/Projects/xray/chexnet/setup3.5/lib/python3.5/site-packages/torch/nn/modules/module.py", line 180, in add_module
    raise KeyError("module name can't contain \".\"")
KeyError: 'module name can\'t contain "."'

So I have upgraded torchvision to 0.2.2. and torch==1.1.0. and my train went successful. When I try to run denseNet_localization.py file then I got the above error.

Hello @rajdeinno how did u solve this error please healp me in this regard. Thanks @rajdeinno

check this. https://github.com/thtang/CheXNet-with-localization/issues/7#issuecomment-514562151

Aliktk commented 3 years ago

Hi Tang, I am able to generate the bound_box.txt file after I execute the denseNet_localization.pyfile. how to visualize the bound box text file into the input image? as you mentioned in ground-truth label (red) and its prediction (blue). Thanks in advance.. Please assist me on this.. … Sent from my iPhone On 28-May-2019, at 17:57, T.H. Tang @.***> wrote: It seem that the errors are just caused by the different version of packages. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

@rajdeinno hello sir after generating BB file how you print BB on that image with heatmap of that image? Pleae help