Leginon

h1. Setup Ptolemy CLI shell script for Square Finding

The script needs to take three variables

# the output json file name without the extension

# input mrc file path

# the directory that contains the grid tile mrc file.  This is redundant information, but is kept to give consistent 3 option input as the Hole Finding script

* Within Leginon MosaicExternalScoreFinder instance defines, for each incoming gr image, a unique name from mosaic label and image id to form the value of variable 1.

Here is an example of this shell script we call sq_finding.sh

<pre>

#!/bin/sh -f

#python3 /your_ptlomy/bin/runPtolemyLmm.py $1 $2 $3

# This runs ptolemy locally using conda environment.

source /usr/local/anaconda3/etc/profile.d/conda.sh

conda activate /opt/condaenvs/ptolemy_env

# variable 1 is the outputname without json extension

# variable 2 is the input mrc path

# variable 3 is the directory that contains the grid tile mrc file

echo $1

echo $2

mrc_path=$2

python /your/ptolemy/ptolemy/lowmag_cli.py -f json $2 > $1

conda deactivate

mv $1 ${mrc_path%%rawdata/*}rawdata/$1.json

echo ${mrc_path%%rawdata/*}rawdata/$1.json

</pre>

Test example, assuming you have /data/leginon/22feb28a/rawdata/22feb28a_00001gr.mrc, you can test ptolemy with

<pre>

./sq_finding.sh test_1 /data/leginon/22feb28a/rawdata/22feb28a_00001gr.mrc dummy

</pre>

Output test_1.json should end up in /data/leginon/22feb28a/rawdata/