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Computational Endoscopy Platform (advanced deep learning toolset for analyzing endoscopy videos) [MICCAI'22, MICCAI'21, ISBI'21, CVPR'20]

License: Other

Dockerfile 0.69% Python 99.31%
area-coverage colonoscopy computer-vision deep-learning domain-adaptation endoscopy gan pytorch real2sim segmentation sim2real tracking unsupervised-learning videos

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cep's Issues

Training error - RuntimeError: The size of tensor a (128) must match the size of tensor b (160)

Hi, Following your instructions I am trying to train CLTS-GAN on the public dataset oldIt_public_data.

My input arguments are as follows:

--dataroot ./Data/cep/FoldIt_public --model cltsgan --name "cltsgan_model_name"

I get the following error

Traceback (most recent call last):
  File "/snap/pycharm-professional/306/plugins/python/helpers/pydev/pydevd.py", line 1496, in _exec
    pydev_imports.execfile(file, globals, locals)  # execute the script
  File "/snap/pycharm-professional/306/plugins/python/helpers/pydev/_pydev_imps/_pydev_execfile.py", line 18, in execfile
    exec(compile(contents+"\n", file, 'exec'), glob, loc)
  File "/home/eposner/Repositories/CEP/train.py", line 51, in <module>
    model.optimize_parameters()   # calculate loss functions, get gradients, update network weights
  File "/home/eposner/Repositories/CEP/models/cltsgan_model.py", line 262, in optimize_parameters
    self.forward()      # compute fake images and reconstruction images.
  File "/home/eposner/Repositories/CEP/models/cltsgan_model.py", line 136, in forward
    self.rec_A   = self.netG_B(self.fake_B, self.nfake_B, self.tfake_B)   # G_B(G_A(A))
  File "/home/eposner/anaconda3/envs/CEP/lib/python3.6/site-packages/torch/nn/modules/module.py", line 532, in __call__
    result = self.forward(*input, **kwargs)
  File "/home/eposner/Repositories/CEP/models/networks.py", line 619, in forward
    out = out + self.n_parm[i] * n
RuntimeError: The size of tensor a (128) must match the size of tensor b (160) at non-singleton dimension 1

I found out the setting --ngf 80 solves this (just like in the googlecolab notebook).
Consider setting it a default value for the dataset?

FoldIt test data

Hi,
I would like to get the IoU and Dice metrics as done in the FoldIt paper (Table 1), however I cannot find the two sequences that you used to get these metrics. Could you please tell me where I could find them or are they not available?
Thank you

Data issue

Training data and test data cannot be downloaded

About augment in the CLTS-GAN

When I read your paper of CLTS-GAN, I found that there was an experiment in which one OC diagram was used to enhance the other one, but I could not find the corresponding part in your code. Could you please tell me how to test this part?
Besides, how does the triple augment work in the paper?
Looking forward to your reply!

CLTS-GAN Test wrong

When I use the pre-trained model to test the CLTS-GAN,I meet the problem, which is also happened when I use my model to test.
Can you tell me the reason, please?
thanks!

RuntimeError: Error(s) in loading state_dict for invResnetGenerator:
Missing key(s) in state_dict: "model.10.conv_block.6.weight", "model.10.conv_block.6.bias", "model.11.conv_block.6.weight", "model.11.conv_block.6.bias", "model.12.conv_block.6.weight", "model.12.conv_block.6.bias", "model.13.conv_block.6.weight", "model.13.conv_block.6.bias", "model.14.conv_block.6.weight", "model.14.conv_block.6.bias", "model.15.conv_block.6.weight", "model.15.conv_block.6.bias", "model.16.conv_block.6.weight", "model.16.conv_block.6.bias", "model.17.conv_block.6.weight", "model.17.conv_block.6.bias", "model.18.conv_block.6.weight", "model.18.conv_block.6.bias".
Unexpected key(s) in state_dict: "model.10.conv_block.5.weight", "model.10.conv_block.5.bias", "model.11.conv_block.5.weight", "model.11.conv_block.5.bias", "model.12.conv_block.5.weight", "model.12.conv_block.5.bias", "model.13.conv_block.5.weight", "model.13.conv_block.5.bias", "model.14.conv_block.5.weight", "model.14.conv_block.5.bias", "model.15.conv_block.5.weight", "model.15.conv_block.5.bias", "model.16.conv_block.5.weight", "model.16.conv_block.5.bias", "model.17.conv_block.5.weight", "model.17.conv_block.5.bias", "model.18.conv_block.5.weight", "model.18.conv_block.5.bias".

ABOUT OC-depth

hiiiii,Thank you for your contribution.
Do you have OC map for depth? (original image)
Looking forward to your reply.

train foldit model

Hello, I have some question about the training command. Does "foldit_model_name" in training command represent the concrete model name? Like 'foldit_model_public/latest_net_G_A.pth'.

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