denoise training using tif format movie file about topaz

[tbepler]

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]

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]

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]

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]

Thanks for your help. This problem has been solved by the solution you gave. Best, Ning 从 Windows 版邮件<https://go.microsoft.com/fwlink/?LinkId=550986>发送 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-2022<https://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. ― Reply to this email directly, view it on GitHub<#148 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AZS5ZQEZB3TCX2KMJETGMQDVRW6WXANCNFSM5YRFHE6A>. You are receiving this because you were mentioned.Message ID: ***@***.***>