Leginon

h1. 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

<pre>

#!/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

</pre>

h3. Testing example

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

<pre>

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

</pre>

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.