batch_zplsc_whoi_singleprocess.sh

#!/bin/bash
#
# Setup a batch processing job for the recovered data from an uncabled AZFP
# bioacoustic sonar sensor.
#
# C. Wingard 2021-11-10

# Parse the command line inputs, setting the data directories and processing dates
if [ $# -ne 5 ]; then
    echo "$0: required inputs are the site name, the path to the raw and processed data"
    echo "directories, and the starting and ending dates (format is YYYY-MM-DD) of the"
    echo "deployment to batch process."
    echo ""
    echo "    example: $0 ce07shsm /home/ooiuser/data/CE07SHSM/R00010/instrmts/dcl37/ZPLSC_sn55099/DATA \\ "
    echo "        /home/ooiuser/data/CE07SHSM/R00010/instrmts/dcl37/ZPLSC_sn55099/processed \\ "
    echo "        \"2019-10-10\" \"2020-07-16\""
    exit 1
fi
SITE=${1^^}
DATA_DIR=$2
PROC_DIR=$3
START_DATE=`date -u +%Y%m%d -d $4`
END_DATE=`date -u +%Y%m%d -d $5`

XML_FILE="${DATA_DIR}/*.XML"

# Tell python where to look for the library...
#export PYTHONPATH=$PYTHONPATH:$HOME/ooi-zpls-echograms/ooi_zpls_echograms

# activate the echopype environment and cd to the ooi_zpls_echograms code directory
# . $(dirname $CONDA_EXE)/../etc/profile.d/conda.sh
source activate echopype
cd /home/ooiuser/ooi-zpls-echograms/ooi_zpls_echograms

# process the data, using 2012-01-01 as the base year for all plots
for d in $(seq $(date -u +%s -d "2012-01-01") +604800 $(date -u +%s -d $END_DATE)); do
    start_date=`date -u +%Y%m%d -d @$d`
    stop_date=`date -u +%Y%m%d -d "$start_date+7days"`
    if [[ $stop_date -gt $START_DATE ]]; then 
        ./zpls_echogram.py -s $SITE -d $DATA_DIR -o $PROC_DIR -dr $start_date $stop_date -zm AZFP -xf $XML_FILE
    fi
done