guzaiwang / ce-net Goto Github PK
View Code? Open in Web Editor NEWThe manuscript has been accepted in TMI.
The manuscript has been accepted in TMI.
First of all, I would like to thank you for disclosing your own code, which can give me a chance to learn. After practice your code, I have one question about
`
class MulticlassDiceLoss(nn.Module):
"""
requires one hot encoded target. Applies DiceLoss on each class iteratively.
requires input.shape[0:1] and target.shape[0:1] to be (N, C) where N is
batch size and C is number of classes
"""
def init(self):
super(MulticlassDiceLoss, self).__init__()
def forward(self, input, target, weights=None):
C = target.shape[1]
totalLoss = 0
for i in range(C):
diceLoss = dice(input[:, i, :, :], target[:, i, :, :])
if weights is not None:
diceLoss *= weights[i]
totalLoss += diceLoss
return totalLoss
`,
the 'input' is ground truth,it has only one channel,how to transform the channel into channels which are equal to the predicted segmentation image?
Could you release TTA(test time augument) code?
Hello, thanks for sharing the code, I am trying to test the network on different medical images with different numbers of input channels, after reading the code, I think the network does not accept images that do not have 3 channels, even though I may be wrong , but I would like to hear from you if it really is.
Hello, I am trying to run the script however I am getting the same error on two different machines
(torch-kernel) mb01761@heron158:/research/CE-Net/src$ python main.py
/conda/.conda/envs/torch-kernel/lib/python3.10/site-packages/scipy/init.py:146: UserWarning: A NumPy version >=1.16.5 and <1.23.0 is required for this version of SciPy (detected version 1.23.4
warnings.warn(f"A NumPy version >={np_minversion} and <{np_maxversion}"
GPUS device is [0]
training chunk_sizes: [24]
The output will be saved to /data/UBT_Seg/binSeg/ORIGA_OD_cenet_dice_bce_loss
Traceback (most recent call last):
File "/vol/research/Neurocomp/mb01761/research/CE-Net/src/main.py", line 126, in
main(opt)
File "/vol/research/Neurocomp/mb01761/research/CE-Net/src/main.py", line 40, in main
logger = Logger(opt)
File "/vol/research/Neurocomp/mb01761/research/CE-Net/src/lib/logger.py", line 25, in init
os.makedirs(opt.save_dir)
File "/vol/research/TopDownVideo/mb01761/conda/.conda/envs/torch-kernel/lib/python3.10/os.py", line 215, in makedirs
makedirs(head, exist_ok=exist_ok)
File "/vol/research/TopDownVideo/mb01761/conda/.conda/envs/torch-kernel/lib/python3.10/os.py", line 215, in makedirs
makedirs(head, exist_ok=exist_ok)
File "/vol/research/TopDownVideo/mb01761/conda/.conda/envs/torch-kernel/lib/python3.10/os.py", line 215, in makedirs
makedirs(head, exist_ok=exist_ok)
File "/vol/research/TopDownVideo/mb01761/conda/.conda/envs/torch-kernel/lib/python3.10/os.py", line 225, in makedirs
mkdir(name, mode)
PermissionError: [Errno 13] Permission denied: '/data'
RuntimeError: The size of tensor a (38) must match the size of tensor b (37) at non-singleton dimension 2
在运行test_center中d4 = self.decoder4(e4) + e3时,pycharm报错,请问有人知道原因吗?非常感谢
Hi! Could you please provide Set_A.txt and Set_B.txt for experiment on ORIGA dataset? I searched online for how ORIGA dataset was divided into training set and test set, but found nothing. According to your data.py, Set_A.txt and Set_B.txt are used to divide ORIGA dataset, so I would be appreciated if you could provide them. Thx!
I run the python -m visdom.server command in the anaconda3 environment and connect to the web page, but then I can’t continue to operate. What is going on?
I can see the data augmentation in Readme.
But I can‘t find the data.py in your fold.
RuntimeError: Error(s) in loading state_dict for CE_Net_:
Missing key(s) in state_dict:
"firstconv.weight", "firstbn.weight", "firstbn.bias", "firstbn.running_mean", "firstbn.running_var", "encoder1.0.conv1.weight", "encoder1.0.bn1.weight", "encoder1.0.bn1.bias", "encoder1.0.bn1.running_mean", "encoder1.0.bn1.running_var", "encoder1.0.conv2.weight", "encoder1.0.bn2.weight", "encoder1.0.bn2.bias", "encoder1.0.bn2.running_mean", "encoder1.0.bn2.running_var", "encoder1.1.conv1.weight", "encoder1.1.bn1.weight", "encoder1.1.bn1.bias", "encoder1.1.bn1.running_mean", "encoder1.1.bn1.running_var", "encoder1.1.conv2.weight", "encoder1.1.bn2.weight", "encoder1.1.bn2.bias", "encoder1.1.bn2.running_mean", "encoder1.1.bn2.running_var", "encoder1.2.conv1.weight", "encoder1.2.bn1.weight", "encoder1.2.bn1.bias", "encoder1.2.bn1.running_mean", "encoder1.2.bn1.running_var", "encoder1.2.conv2.weight", "encoder1.2.bn2.weight", "encoder1.2.bn2.bias", "encoder1.2.bn2.running_mean", "encoder1.2.bn2.running_var", "encoder2.0.conv1.weight", "encoder2.0.bn1.weight", "encoder2.0.bn1.bias", "encoder2.0.bn1.running_mean", "encoder2.0.bn1.running_var", "encoder2.0.conv2.weight", "encoder2.0.bn2.weight", "encoder2.0.bn2.bias", "encoder2.0.bn2.running_mean", "encoder2.0.bn2.running_var", "encoder2.0.downsample.0.weight", "encoder2.0.downsample.1.weight", "encoder2.0.downsample.1.bias", "encoder2.0.downsample.1.running_mean", "encoder2.0.downsample.1.running_var", "encoder2.1.conv1.weight", "encoder2.1.bn1.weight", "encoder2.1.bn1.bias", "encoder2.1.bn1.running_mean", "encoder2.1.bn1.running_var", "encoder2.1.conv2.weight", "encoder2.1.bn2.weight", "encoder2.1.bn2.bias", "encoder2.1.bn2.running_mean", "encoder2.1.bn2.running_var", "encoder2.2.conv1.weight", "encoder2.2.bn1.weight", "encoder2.2.bn1.bias", "encoder2.2.bn1.running_mean", "encoder2.2.bn1.running_var", "encoder2.2.conv2.weight", "encoder2.2.bn2.weight", "encoder2.2.bn2.bias", "encoder2.2.bn2.running_mean", "encoder2.2.bn2.running_var", "encoder2.3.conv1.weight", "encoder2.3.bn1.weight", "encoder2.3.bn1.bias", "encoder2.3.bn1.running_mean", "encoder2.3.bn1.running_var", "encoder2.3.conv2.weight", "encoder2.3.bn2.weight", "encoder2.3.bn2.bias", "encoder2.3.bn2.running_mean", "encoder2.3.bn2.running_var", "encoder3.0.conv1.weight", "encoder3.0.bn1.weight", "encoder3.0.bn1.bias", "encoder3.0.bn1.running_mean", "encoder3.0.bn1.running_var", "encoder3.0.conv2.weight", "encoder3.0.bn2.weight", "encoder3.0.bn2.bias", "encoder3.0.bn2.running_mean", "encoder3.0.bn2.running_var", "encoder3.0.downsample.0.weight", "encoder3.0.downsample.1.weight", "encoder3.0.downsample.1.bias", "encoder3.0.downsample.1.running_mean", "encoder3.0.downsample.1.running_var", "encoder3.1.conv1.weight", "encoder3.1.bn1.weight", "encoder3.1.bn1.bias", "encoder3.1.bn1.running_mean", "encoder3.1.bn1.running_var", "encoder3.1.conv2.weight", "encoder3.1.bn2.weight", "encoder3.1.bn2.bias", "encoder3.1.bn2.running_mean", "encoder3.1.bn2.running_var", "encoder3.2.conv1.weight", "encoder3.2.bn1.weight", "encoder3.2.bn1.bias", "encoder3.2.bn1.running_mean", "encoder3.2.bn1.running_var", "encoder3.2.conv2.weight", "encoder3.2.bn2.weight", "encoder3.2.bn2.bias", "encoder3.2.bn2.running_mean", "encoder3.2.bn2.running_var", "encoder3.3.conv1.weight", "encoder3.3.bn1.weight", "encoder3.3.bn1.bias", "encoder3.3.bn1.running_mean", "encoder3.3.bn1.running_var", "encoder3.3.conv2.weight", "encoder3.3.bn2.weight", "encoder3.3.bn2.bias", "encoder3.3.bn2.running_mean", "encoder3.3.bn2.running_var", "encoder3.4.conv1.weight", "encoder3.4.bn1.weight", "encoder3.4.bn1.bias", "encoder3.4.bn1.running_mean", "encoder3.4.bn1.running_var", "encoder3.4.conv2.weight", "encoder3.4.bn2.weight", "encoder3.4.bn2.bias", "encoder3.4.bn2.running_mean", "encoder3.4.bn2.running_var", "encoder3.5.conv1.weight", "encoder3.5.bn1.weight", "encoder3.5.bn1.bias", "encoder3.5.bn1.running_mean", "encoder3.5.bn1.running_var", "encoder3.5.conv2.weight", "encoder3.5.bn2.weight", "encoder3.5.bn2.bias", "encoder3.5.bn2.running_mean", "encoder3.5.bn2.running_var", "encoder4.0.conv1.weight", "encoder4.0.bn1.weight", "encoder4.0.bn1.bias", "encoder4.0.bn1.running_mean", "encoder4.0.bn1.running_var", "encoder4.0.conv2.weight", "encoder4.0.bn2.weight", "encoder4.0.bn2.bias", "encoder4.0.bn2.running_mean", "encoder4.0.bn2.running_var", "encoder4.0.downsample.0.weight", "encoder4.0.downsample.1.weight", "encoder4.0.downsample.1.bias", "encoder4.0.downsample.1.running_mean", "encoder4.0.downsample.1.running_var", "encoder4.1.conv1.weight", "encoder4.1.bn1.weight", "encoder4.1.bn1.bias", "encoder4.1.bn1.running_mean", "encoder4.1.bn1.running_var", "encoder4.1.conv2.weight", "encoder4.1.bn2.weight", "encoder4.1.bn2.bias", "encoder4.1.bn2.running_mean", "encoder4.1.bn2.running_var", "encoder4.2.conv1.weight", "encoder4.2.bn1.weight", "encoder4.2.bn1.bias", "encoder4.2.bn1.running_mean", "encoder4.2.bn1.running_var", "encoder4.2.conv2.weight", "encoder4.2.bn2.weight", "encoder4.2.bn2.bias", "encoder4.2.bn2.running_mean", "encoder4.2.bn2.running_var", "dblock.dilate1.weight", "dblock.dilate1.bias", "dblock.dilate2.weight", "dblock.dilate2.bias", "dblock.dilate3.weight", "dblock.dilate3.bias", "dblock.conv1x1.weight", "dblock.conv1x1.bias", "spp.conv.weight", "spp.conv.bias", "decoder4.conv1.weight", "decoder4.conv1.bias", "decoder4.norm1.weight", "decoder4.norm1.bias", "decoder4.norm1.running_mean", "decoder4.norm1.running_var", "decoder4.deconv2.weight", "decoder4.deconv2.bias", "decoder4.norm2.weight", "decoder4.norm2.bias", "decoder4.norm2.running_mean", "decoder4.norm2.running_var", "decoder4.conv3.weight", "decoder4.conv3.bias", "decoder4.norm3.weight", "decoder4.norm3.bias", "decoder4.norm3.running_mean", "decoder4.norm3.running_var", "decoder3.conv1.weight", "decoder3.conv1.bias", "decoder3.norm1.weight", "decoder3.norm1.bias", "decoder3.norm1.running_mean", "decoder3.norm1.running_var", "decoder3.deconv2.weight", "decoder3.deconv2.bias", "decoder3.norm2.weight", "decoder3.norm2.bias", "decoder3.norm2.running_mean", "decoder3.norm2.running_var", "decoder3.conv3.weight", "decoder3.conv3.bias", "decoder3.norm3.weight", "decoder3.norm3.bias", "decoder3.norm3.running_mean", "decoder3.norm3.running_var", "decoder2.conv1.weight", "decoder2.conv1.bias", "decoder2.norm1.weight", "decoder2.norm1.bias", "decoder2.norm1.running_mean", "decoder2.norm1.running_var", "decoder2.deconv2.weight", "decoder2.deconv2.bias", "decoder2.norm2.weight", "decoder2.norm2.bias", "decoder2.norm2.running_mean", "decoder2.norm2.running_var", "decoder2.conv3.weight", "decoder2.conv3.bias", "decoder2.norm3.weight", "decoder2.norm3.bias", "decoder2.norm3.running_mean", "decoder2.norm3.running_var", "decoder1.conv1.weight", "decoder1.conv1.bias", "decoder1.norm1.weight", "decoder1.norm1.bias", "decoder1.norm1.running_mean", "decoder1.norm1.running_var", "decoder1.deconv2.weight", "decoder1.deconv2.bias", "decoder1.norm2.weight", "decoder1.norm2.bias", "decoder1.norm2.running_mean", "decoder1.norm2.running_var", "decoder1.conv3.weight", "decoder1.conv3.bias", "decoder1.norm3.weight", "decoder1.norm3.bias", "decoder1.norm3.running_mean", "decoder1.norm3.running_var", "finaldeconv1.weight", "finaldeconv1.bias", "finalconv2.weight", "finalconv2.bias", "finalconv3.weight", "finalconv3.bias".
Unexpected key(s) in state_dict: "module.firstconv.weight", "module.firstbn.weight", "module.firstbn.bias", "module.firstbn.running_mean", "module.firstbn.running_var", "module.firstbn.num_batches_tracked", "module.encoder1.0.conv1.weight", "module.encoder1.0.bn1.weight", "module.encoder1.0.bn1.bias", "module.encoder1.0.bn1.running_mean", "module.encoder1.0.bn1.running_var", "module.encoder1.0.bn1.num_batches_tracked", "module.encoder1.0.conv2.weight", "module.encoder1.0.bn2.weight", "module.encoder1.0.bn2.bias", "module.encoder1.0.bn2.running_mean", "module.encoder1.0.bn2.running_var", "module.encoder1.0.bn2.num_batches_tracked", "module.encoder1.1.conv1.weight", "module.encoder1.1.bn1.weight", "module.encoder1.1.bn1.bias", "module.encoder1.1.bn1.running_mean", "module.encoder1.1.bn1.running_var", "module.encoder1.1.bn1.num_batches_tracked", "module.encoder1.1.conv2.weight", "module.encoder1.1.bn2.weight", "module.encoder1.1.bn2.bias", "module.encoder1.1.bn2.running_mean", "module.encoder1.1.bn2.running_var", "module.encoder1.1.bn2.num_batches_tracked", "module.encoder1.2.conv1.weight", "module.encoder1.2.bn1.weight", "module.encoder1.2.bn1.bias", "module.encoder1.2.bn1.running_mean", "module.encoder1.2.bn1.running_var", "module.encoder1.2.bn1.num_batches_tracked", "module.encoder1.2.conv2.weight", "module.encoder1.2.bn2.weight", "module.encoder1.2.bn2.bias", "module.encoder1.2.bn2.running_mean", "module.encoder1.2.bn2.running_var", "module.encoder1.2.bn2.num_batches_tracked", "module.encoder2.0.conv1.weight", "module.encoder2.0.bn1.weight", "module.encoder2.0.bn1.bias", "module.encoder2.0.bn1.running_mean", "module.encoder2.0.bn1.running_var", "module.encoder2.0.bn1.num_batches_tracked", "module.encoder2.0.conv2.weight", "module.encoder2.0.bn2.weight", "module.encoder2.0.bn2.bias", "module.encoder2.0.bn2.running_mean", "module.encoder2.0.bn2.running_var", "module.encoder2.0.bn2.num_batches_tracked", "module.encoder2.0.downsample.0.weight", "module.encoder2.0.downsample.1.weight", "module.encoder2.0.downsample.1.bias", "module.encoder2.0.downsample.1.running_mean", "module.encoder2.0.downsample.1.running_var", "module.encoder2.0.downsample.1.num_batches_tracked", "module.encoder2.1.conv1.weight", "module.encoder2.1.bn1.weight", "module.encoder2.1.bn1.bias", "module.encoder2.1.bn1.running_mean", "module.encoder2.1.bn1.running_var", "module.encoder2.1.bn1.num_batches_tracked", "module.encoder2.1.conv2.weight", "module.encoder2.1.bn2.weight", "module.encoder2.1.bn2.bias", "module.encoder2.1.bn2.running_mean", "module.encoder2.1.bn2.running_var", "module.encoder2.1.bn2.num_batches_tracked", "module.encoder2.2.conv1.weight", "module.encoder2.2.bn1.weight", "module.encoder2.2.bn1.bias", "module.encoder2.2.bn1.running_mean", "module.encoder2.2.bn1.running_var", "module.encoder2.2.bn1.num_batches_tracked", "module.encoder2.2.conv2.weight", "module.encoder2.2.bn2.weight", "module.encoder2.2.bn2.bias", "module.encoder2.2.bn2.running_mean", "module.encoder2.2.bn2.running_var", "module.encoder2.2.bn2.num_batches_tracked", "module.encoder2.3.conv1.weight", "module.encoder2.3.bn1.weight", "module.encoder2.3.bn1.bias", "module.encoder2.3.bn1.running_mean", "module.encoder2.3.bn1.running_var", "module.encoder2.3.bn1.num_batches_tracked", "module.encoder2.3.conv2.weight", "module.encoder2.3.bn2.weight", "module.encoder2.3.bn2.bias", "module.encoder2.3.bn2.running_mean", "module.encoder2.3.bn2.running_var", "module.encoder2.3.bn2.num_batches_tracked", "module.encoder3.0.conv1.weight", "module.encoder3.0.bn1.weight", "module.encoder3.0.bn1.bias", "module.encoder3.0.bn1.running_mean", "module.encoder3.0.bn1.running_var", "module.encoder3.0.bn1.num_batches_tracked", "module.encoder3.0.conv2.weight", "module.encoder3.0.bn2.weight", "module.encoder3.0.bn2.bias", "module.encoder3.0.bn2.running_mean", "module.encoder3.0.bn2.running_var", "module.encoder3.0.bn2.num_batches_tracked", "module.encoder3.0.downsample.0.weight", "module.encoder3.0.downsample.1.weight", "module.encoder3.0.downsample.1.bias", "module.encoder3.0.downsample.1.running_mean", "module.encoder3.0.downsample.1.running_var", "module.encoder3.0.downsample.1.num_batches_tracked", "module.encoder3.1.conv1.weight", "module.encoder3.1.bn1.weight", "module.encoder3.1.bn1.bias", "module.encoder3.1.bn1.running_mean", "module.encoder3.1.bn1.running_var", "module.encoder3.1.bn1.num_batches_tracked", "module.encoder3.1.conv2.weight", "module.encoder3.1.bn2.weight", "module.encoder3.1.bn2.bias", "module.encoder3.1.bn2.running_mean", "module.encoder3.1.bn2.running_var", "module.encoder3.1.bn2.num_batches_tracked", "module.encoder3.2.conv1.weight", "module.encoder3.2.bn1.weight", "module.encoder3.2.bn1.bias", "module.encoder3.2.bn1.running_mean", "module.encoder3.2.bn1.running_var", "module.encoder3.2.bn1.num_batches_tracked", "module.encoder3.2.conv2.weight", "module.encoder3.2.bn2.weight", "module.encoder3.2.bn2.bias", "module.encoder3.2.bn2.running_mean", "module.encoder3.2.bn2.running_var", "module.encoder3.2.bn2.num_batches_tracked", "module.encoder3.3.conv1.weight", "module.encoder3.3.bn1.weight", "module.encoder3.3.bn1.bias", "module.encoder3.3.bn1.running_mean", "module.encoder3.3.bn1.running_var", "module.encoder3.3.bn1.num_batches_tracked", "module.encoder3.3.conv2.weight", "module.encoder3.3.bn2.weight", "module.encoder3.3.bn2.bias", "module.encoder3.3.bn2.running_mean", "module.encoder3.3.bn2.running_var", "module.encoder3.3.bn2.num_batches_tracked", "module.encoder3.4.conv1.weight", "module.encoder3.4.bn1.weight", "module.encoder3.4.bn1.bias", "module.encoder3.4.bn1.running_mean", "module.encoder3.4.bn1.running_var", "module.encoder3.4.bn1.num_batches_tracked", "module.encoder3.4.conv2.weight", "module.encoder3.4.bn2.weight", "module.encoder3.4.bn2.bias", "module.encoder3.4.bn2.running_mean", "module.encoder3.4.bn2.running_var", "module.encoder3.4.bn2.num_batches_tracked", "module.encoder3.5.conv1.weight", "module.encoder3.5.bn1.weight", "module.encoder3.5.bn1.bias", "module.encoder3.5.bn1.running_mean", "module.encoder3.5.bn1.running_var", "module.encoder3.5.bn1.num_batches_tracked", "module.encoder3.5.conv2.weight", "module.encoder3.5.bn2.weight", "module.encoder3.5.bn2.bias", "module.encoder3.5.bn2.running_mean", "module.encoder3.5.bn2.running_var", "module.encoder3.5.bn2.num_batches_tracked", "module.encoder4.0.conv1.weight", "module.encoder4.0.bn1.weight", "module.encoder4.0.bn1.bias", "module.encoder4.0.bn1.running_mean", "module.encoder4.0.bn1.running_var", "module.encoder4.0.bn1.num_batches_tracked", "module.encoder4.0.conv2.weight", "module.encoder4.0.bn2.weight", "module.encoder4.0.bn2.bias", "module.encoder4.0.bn2.running_mean", "module.encoder4.0.bn2.running_var", "module.encoder4.0.bn2.num_batches_tracked", "module.encoder4.0.downsample.0.weight", "module.encoder4.0.downsample.1.weight", 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感觉作者的引用不太全呀,还有代码最好写上based on哪个开源代码
已经将
ROOT= './dataset/CamVid'
BINARY_CLASS = 5
改为测试需要的值,并且写好读该数据的函数,测试用的loss为loss.py的MulticlassDiceLoss,因维度问题出现多出报错
N, H, W = target.size(0), target.size(2), target.size(3) IndexError: Dimension out of range (expected to be in range of [-3, 2], but got 3)
修正这个问题后又出现
diceLoss = dice(input[:, i, :, :], target[:, i,:, :]) IndexError: index 1 is out of bounds for dimension 1 with size 1
采用nn.CrossEntropyLoss()为loss,出现
if size_average and reduce: RuntimeError: bool value of Tensor with more than one value is ambiguous
能否上传一份测试多分类分割的示例代码呢
I run test_cenet.py, but i got the all black or all white mask. how can i solve this?
and i want to know where is your pretrained model? Thanks @Guzaiwang
Hi, dear author, thank you for amazing segmentation network CENet and your open source code. I am wondering whether you can release the Retinal OCT layer Dataset for us to follow your work.
I am so proud of you.
Does anyone have the same situation as me? In the process of training the network, the learning rate update directly becomes 0
您好,我在readme中看到您已上传了测试代码,但是我并未找到。
Can I use cpu to run the program? The error is [WinError 10054] An existing connection was forcibly closed by the remote host
Thanks for your effort.
Could you please share your pretrained model?
it seems Unet in your code can outperform CE_Net in my training. I directly used your code and retrained the Unet, I got a accuracy of [acc: 0.956 | sen: 0.844 | auc:0.98]. This should better than the results of CE_Net. could you please share you weights?
Can you configure the environment for the next code? For example, torch version? Thank you
There is no test CE-Net code in main.py?
Hi, I am wondering how to reproduce the retinal vessel segmentation results in the paper with DRIVE dataset, such as the details of training and the inference. Thank you!
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