Deconvolve Error

[Stefan Oliver]

Hi!

After the excellent IsoNet presentation at Wha's group meeting yesterday I wanted to give IsoNet a go.  Unfortunately, I've stumbled across an error at the deconvolve step...

######Isonet starts ctf deconvolve######

11-16 09:51:05, ERROR    Traceback (most recent call last):
  File "/data2/sloliver/IsoNet/bin/isonet.py", line 163, in deconv
    deconv_one(it.rlnMicrographName,deconv_tomo_name,voltage=voltage,cs=cs,defocus=it.rlnDefocus/10000.0, pixel_size=it.rlnPixelSize,snrfalloff=it.rlnSnrFalloff, deconvstrength=it.rlnDeconvStrength,highpassnyquist=highpassnyquist,chunk_size=chunk_size,overlap_rate=overlap_rate,ncpu=ncpu)
TypeError: deconv_one() got an unexpected keyword argument 'voltage'

The contents of my tomogram star file are

data_

loop_
_rlnIndex #1
_rlnMicrographName #2
_rlnPixelSize #3
_rlnDefocus #4
_rlnNumberSubtomo #5
_rlnMaskBoundary #6
1 tomoset/abcapsids20230930_014.mrc 13.760000 46255.000000 100 None
2 tomoset/abcapsids20230930_019.mrc 13.760000 51693.000000 100 None
3 tomoset/abcapsids20230930_021.mrc 13.760000 47137.000000 100 None
4 tomoset/abcapsids20230930_043.mrc 13.760000 59374.000000 100 None
5 tomoset/abcapsids20230930_044.mrc 13.760000 52629.000000 100 None

I hope we can figure this out so I can use this excellent program.

Cheers,

Stefan

[YUNTAO LIU]

Hi Stefan,

I do not have a clue about this error in deconvolution. 

The function "deconv_one" does have the keyword argument 'voltage': "def deconv_one(tomo, out_tomo, voltage=300.0, ... "

I am not sure but my guess is that you might be importing from a version of IsoNet that someone else has modified the code.

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Best Regards,

Yuntao Liu,  Postdoc.

California NanoSystem Institute

University of California Los Angeles

[Hui Wang]

Hi Stefan,

According to Yuntao, you may want to check the file: IsoNet/util/deconvolution.py, see line 180

the deconv_one function should be defined in this format:

def deconv_one(tomo, out_tomo, voltage=300.0, cs=2.7, defocus=1.0, pixel_size=1.0,snrfalloff=1.0, deconvstrength=1.0,highpassnyquist=0.02,chunk_size=200,overlap_rate = 0.25,ncpu=4):

Can you see the voltage parameter there?

Best,

Hui

[Stefan Oliver]

Thanks for the prompt reply, Yuntao.  There was a previous version (0.1) on my Linux machine.  I removed that installation and then did a fresh install of version 0.2 from the downloaded zip file.  Would that cause an issue?

On Thursday, November 16, 2023 at 11:39:20 AM UTC-8 yun...@g.ucla.edu wrote:

[Stefan Oliver]

Hi Hui,

Yes, the parameter is present.

Cheers,

Stefan