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LBEM-CH / focus

High Throughput Electron Microscopy Image Processing Software
http://www.focus-em.org
GNU General Public License v2.0
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ctfapply.py #211

Closed z-watson closed 6 years ago

z-watson commented 6 years ago

Hello,

I am trying to run ctfapply.py on an image from the command line and I am encountering the issue that the corrected micrograph image file is just an image with undefined pixel values for every pixel. If I use the --save_ctf_2d flag, those additional outputs all look fine. I was wondering if there are any suggestions to fix this. I tried both phase flipping and ctf multiplication, but they both had the same problem.

I also notice that I always get this message when I run it, but thought it was probably unrelated:

No handlers could be found for logger "mrcz.test_mrcz"

Thanks, Zoe

rdrighetto commented 6 years ago

Dear Zoe,

Thanks for reporting this bug. There was a problem due to improper memory mapping when reading the input MRC file; I also detected a bug regarding the name of the output file. It has been fixed now. However the way it is now, if you try to apply the CTF correction on a large MRC stack you may run out of memory; for single images and small stacks it works fine. Please note that I recently renamed this script to 'focus.ctfapply'. You can just pull the latest version from GitHub.

Best wishes,

-- Ricardo Diogo Righetto

2018-01-26 23:05 GMT+01:00 z-watson notifications@github.com:

Hello,

I am trying to run ctfapply.py on an image from the command line and I am encountering the issue that the corrected micrograph image file is just an image with undefined pixel values for every pixel. If I use the --save_ctf_2d flag, those additional outputs all look fine. I was wondering if there are any suggestions to fix this. I tried both phase flipping and ctf multiplication, but they both had the same problem.

I also notice that I always get this message when I run it, but thought it was probably unrelated:

No handlers could be found for logger "mrcz.test_mrcz"

Thanks, Zoe

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