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tbepler / topaz

Pipeline for particle picking in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Also featuring micrograph and tomogram denoising with DNNs.
GNU General Public License v3.0
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denoise training using tif format movie file #148

Closed ning-2022 closed 2 years ago

ning-2022 commented 2 years ago

Hi, I have a question about denoise training of topaz, that is how to use the tif format movie file collected from titan krios EM for denoise training. I know that in the tutorial, the author use the mrc format movie file to train the denoise model. Any suggestions are welcome. Thanks in advance!

Ning

tbepler commented 2 years ago

Topaz can parse tif files without any issue. However, denoise train does not work on the movie frames. These need to be aligned and summed first.

ning-2022 commented 2 years ago

Thanks for your help. I had successfully split the movie frames and summed them into two group mrc files. However, a new problem had been appeared when I tried to train the denoise model for micrographs. Here is the error information:

...... 93 0.9685644149780274 0
94 0.9719996452331543 0
95 0.9726578831672669 0
96 0.972616457939148 0
97 0.9692490220069885 0
98 0.971499752998352 0
99 0.9668266415596009 0
100 0.9698738217353821 0
Traceback (most recent call last): File "/home/spuser/WN/anaconda3/envs/topaz/bin/topaz", line 33, in sys.exit(load_entry_point('topaz-em==0.2.5', 'console_scripts', 'topaz')()) File "/home/spuser/WN/anaconda3/envs/topaz/lib/python3.6/site-packages/topaz/main.py", line 148, in main args.func(args) File "/home/spuser/WN/anaconda3/envs/topaz/lib/python3.6/site-packages/topaz/commands/denoise.py", line 535, in main if not os.path.exists(args.output): File "/home/spuser/WN/anaconda3/envs/topaz/lib/python3.6/genericpath.py", line 19, in exists os.stat(path) TypeError: stat: path should be string, bytes, os.PathLike or integer, not NoneType

I just use the command:
topaz denoise -a partA/ -b partB/ --save-prefix models/ Please help me, I'm not good at python programming.

Ning

tbepler commented 2 years ago

Actually, this looks like a bug in topaz denoise. You can work around it by setting the --output flag to a directory name (like --output ./).

Really, when training the denoising model without passing any additional micrographs to denoise, though, we shouldn't require this parameter. @DarnellGranberry can you add a quick check for len(micrographs) < 1 and skip processing if it is to avoid this problem?

DarnellGranberry commented 2 years ago

Just added the check. @ning-2022 if you're using v0.2.5 (from pip/conda), then you will still need to use the workaround Tristan gave; if you installed from source, then you can pull master for the updated lines.

ning-2022 commented 2 years ago

Thanks for your help. This problem has been solved by the solution you gave.

Best,

Ning

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发件人: Darnell @.> 发送时间: 2022年6月30日 23:49 收件人: @.> 抄送: @.>; @.> 主题: Re: [tbepler/topaz] denoise training using tif format movie file (Issue #148)

Just added the check. @ning-2022https://github.com/ning-2022 if you're using v0.2.5 (from pip/conda), then you will still need to use the workaround Tristan gave; if you installed from source, then you can pull master for the updated lines.

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