Published on cisTEM (https://cistem.org)

Launching cisTEM jobs from command line - Exposure filtering

6 posts / 0 new

Mon, 03/25/2019 - 06:29

eugenio.delamora

Hi,

I'am using Unblur to 'dose filter' tilted-series. I would like to do it automatically from the command line, by creating a simple script.

Is it possible? Does cisTEM write the command line for all jobs ?

Many thanks

Eugenio

Mon, 03/25/2019 - 13:13

timgrant

Hi Eugenio,

You can run unblur from the command line, and so you can script it. if you go to the cisTEM bin directory and run ./unblur it will ask you for the inputs as a series of questions. You can script this by piping input to the executable.

Will that do what you want?

Cheers,

Tim

Mon, 03/25/2019 - 13:40

(Reply to #2) #3

eugenio.delamora

I think so

Hi Tim,

Many thanks. Yes, I'll figure out how to do it.

There is no way of setting -input -output -pixel_size -bin -exposure_filer ... ?

Cheers

Eugenio

Mon, 03/25/2019 - 13:41

eugenio.delamora

Exposure filter

I meant -exposure_filter

Actually, what I would like to do is to compare different exposure filtering ways.

Thanks again

Eugenio

Mon, 03/25/2019 - 13:44

timgrant

Hi Eugenio,

You could write a bash script that accepts input, ouput pixel size etc as input and runs unblur with the inputs you need.

Cheers,

Tim

Tue, 03/26/2019 - 04:12

(Reply to #5) #6

eugenio.delamora

Yes, that's what I was

Yes, that's what I was thinking about.

Many thanks again Tim.

Cheers

Eugenio

Source URL:https://cistem.org/launching-cistem-jobs-command-line-exposure-filtering?page=0