Setup Ptolemy CLI for exposure targeting » History » Version 1
Anchi Cheng, 03/15/2022 01:20 PM
1 | 1 | Anchi Cheng | h1. Setup Ptolemy CLI for exposure targeting |
---|---|---|---|
2 | |||
3 | This shell script needs to take three arguments |
||
4 | |||
5 | 1. output json rootname. Leginon will assign this according to the session name and node alias calling this. For example, "22mar15a_Exposure_Targeting" |
||
6 | 2. full input mrc file path. Leginon will assign this according to its session path. For example "/data/leginon/22mar15a/rawdata/22mar15a_00001hl.mrc" |
||
7 | 3. output directory name. Leginon will assign this to the directory where Leginon is launched, assuming write assess of the user. For example, "/home/your_name" |
||
8 | |||
9 | Here is an example script used at SEMC |
||
10 | |||
11 | <pre> |
||
12 | #!/bin/sh -f |
||
13 | # Local runs |
||
14 | source /usr/local/anaconda3/etc/profile.d/conda.sh |
||
15 | conda activate /opt/condaenvs/ptolemy_env |
||
16 | echo $1 |
||
17 | echo $2 |
||
18 | echo $3 |
||
19 | python /home/your_name/packages/ptolemy/medmag_cli.py -f json -o $3/$1.json $2 |
||
20 | conda deactivate |
||
21 | </pre> |
||
22 | |||
23 | During leginon operation, the output json will be read by Leginon into memory and be replaced each time it is run. |