Setup Ptolemy CLI for exposure targeting » History » Revision 1
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Anchi Cheng, 03/15/2022 01:20 PM
Setup Ptolemy CLI for exposure targeting¶
This shell script needs to take three arguments
1. output json rootname. Leginon will assign this according to the session name and node alias calling this. For example, "22mar15a_Exposure_Targeting"
2. full input mrc file path. Leginon will assign this according to its session path. For example "/data/leginon/22mar15a/rawdata/22mar15a_00001hl.mrc"
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"
Here is an example script used at SEMC
#!/bin/sh -f # Local runs source /usr/local/anaconda3/etc/profile.d/conda.sh conda activate /opt/condaenvs/ptolemy_env echo $1 echo $2 echo $3 python /home/your_name/packages/ptolemy/medmag_cli.py -f json -o $3/$1.json $2 conda deactivate
During leginon operation, the output json will be read by Leginon into memory and be replaced each time it is run.
Updated by Anchi Cheng over 2 years ago · 1 revisions