Setup Ptolemy CLI shell script » History » Revision 3
Revision 2 (Anchi Cheng, 03/15/2022 12:53 PM) → Revision 3/5 (Anchi Cheng, 09/27/2022 04:14 PM)
h1. Setup Ptolemy CLI shell script for Square Finding The script needs to take three variables two options # 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. image: Here is an example of this shell script we call sq_finding.sh <pre> #!/bin/sh -f #python3 /emg/sw/bin/runPtolemyLmm.py $1 $2 $3 # This Local 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 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 /h/acheng/site-packages/ptolemy/lowmag_cli.py /home/your_name/packages/ptolemy/lowmag_cli.py -f json $2 > $1 conda deactivate # mv the result to leginon session rawdata directory 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/