Question regarding how to use --continuefrom

[Maia Azubel]

I've done only one iteration (p) with e2spt_refine_new.py. 

I got aliptcls2d_01.lst, aliptcls3d_01.lst, threed_01.hdf

I wanted to continue from where it finished.

And I tried to use continue_from in the following way

e2spt_refine_new.py --path spt_196 --continuefrom 1 --sym=c1 --loadali2d spt_196/aliptcls2d_01.lst --iters=p --keep=0.95 --tophat=localwiener

But I get the following message

Processing 3685466 images in spt_196/aliptcls2d_01.lst

Writing in spt_196...

Using existing metadata files within the directory...

last 3d alignment: spt_196/aliptcls3d_01.lst

last 2d alignment: None

e2proclst.py spt_196/aliptcls2d_01.lst --create spt_196/aliptcls2d_00.lst

and fails. 

Why is it: last 2d alignment: None?

What's the correct way to use continue_from to pick it up from where it finished?

Thanks, 

Maia

[Muyuan Chen]

Hi Maia, 

Last 2d alignment is None because it only reads the 2D subtilt alignment. If there hasn't been a 't' or 'r' iteration previously, it is normal for it to be None. It will just use the 2d alignment of the tilt series. I think the --loadali2d option is not compatible with --continuefrom, and removing it should be safer. The main issue of the command you ran is it says --iters=p only. You asked for 1 iteration in total and 1 iteration has already finished, so as expected, it will do nothing... Try --iters=p5 or something and see if it moves forward.

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