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

Testing example¶

Assuming you have /data/leginon/22mar15a/rawdata/22mar15a_00001hl.mrc, and call the above script hl_finding.sh you can test with

hl_finding.sh my_test /data/leginon/22mar15a/rawdata/22mar15a_00001hl.mrc .

You should get my_test.json written in your current directory.

During leginon operation, the output json will be read by Leginon into memory and be replaced each time it is run.