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Generate celery task commands for serializing IDR images to avro
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#!/bin/bash | |
set -eu | |
shopt -s nullglob | |
AVRO_PARENTDIR=/uod/idr/homes/szleo/features/idr0012-fuchs-cellmorph/screenA/input | |
IDR_WRITEABLE=/home/idr-scratch/szleo | |
RUNAS_USER=13500 | |
ADD_TASK="../venv/bin/python tasks.py" | |
TASKID_LOG=taskid-calc.log | |
TILE_WIDTH=168 | |
TILE_HEIGHT=128 | |
RUN=0 | |
if [ "${1:-}" = "-run" ]; then | |
RUN=1 | |
fi | |
if [ ! -f tasks.py ]; then | |
echo "ERROR: Must be run from the celery-example directory" | |
exit 2 | |
fi | |
if [ -f "$TASKID_LOG" ]; then | |
echo "ERROR: \$TASKID_LOG=$TASKID_LOG already exists, delete or rename it" | |
exit 2 | |
fi | |
echoruntee() { | |
echo "$@" | |
if [ $RUN -eq 1 ]; then | |
"$@" | tee -a "$TASKID_LOG" | |
fi | |
} | |
count=0 | |
TESTING_LIMIT=0 | |
for parent in "${AVRO_PARENTDIR}/"*; do | |
for avro in "${parent}"/*.avro; do | |
screen_name="$(basename "${parent}")" | |
avro_bn="$(basename "${avro}")" | |
log_tag="${avro_bn%.*}" | |
count=$((count + 1)) | |
echoruntee ${ADD_TASK} \ | |
"${IDR_WRITEABLE}/out/${screen_name}/${log_tag}.out" \ | |
"${IDR_WRITEABLE}/out/${screen_name}/${log_tag}.err" \ | |
docker run --rm -u "${RUNAS_USER}" \ | |
-v /uod/idr:/uod/idr:ro \ | |
-v "${IDR_WRITEABLE}:/scratch" \ | |
simleo/pyfeatures \ | |
calc \ | |
"${avro}" \ | |
-l -W ${TILE_WIDTH} -H ${TILE_HEIGHT} \ | |
-o "/scratch/out/${screen_name}" | |
# Use = so that we can easily disable by setting TESTING_LIMIT=0 | |
if [ "$TESTING_LIMIT" = "$count" ]; then | |
break 2 | |
fi | |
done | |
done |
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#!/bin/bash | |
set -eu | |
IDR_METADATA=/uod/idr/homes/scratch/szleo/idr-metadata/idr0012-fuchs-cellmorph/screenA | |
#IDR_TSV=idr0012-screenA-plates.tsv | |
IDR_TSV=idr0012-screenA-plates.tsv.small | |
IDR_WRITEABLE=/home/idr-scratch/szleo | |
#RUNAS_USER=13500 | |
RUNAS_USER=1000 | |
ADD_TASK="../venv/bin/python tasks.py" | |
TASKID_LOG=taskid-serialize.log | |
RUN=0 | |
if [ "${1:-}" = "-run" ]; then | |
RUN=1 | |
fi | |
if [ ! -f tasks.py ]; then | |
echo "ERROR: Must be run from the celery-example directory" | |
exit 2 | |
fi | |
if [ -f "$TASKID_LOG" ]; then | |
echo "ERROR: \$TASKID_LOG=$TASKID_LOG already exists, delete or rename it" | |
exit 2 | |
fi | |
echoruntee() { | |
echo "$@" | |
if [ $RUN -eq 1 ]; then | |
"$@" | tee -a "$TASKID_LOG" | |
fi | |
} | |
while IFS=$'\t' read -r -a arr; do | |
screen_name="${arr[0]}" | |
screen_file="${arr[1]}" | |
echoruntee ${ADD_TASK} \ | |
"${IDR_WRITEABLE}/out/${screen_name}.out" \ | |
"${IDR_WRITEABLE}/out/${screen_name}.err" \ | |
docker run --rm -u "${RUNAS_USER}" \ | |
-v /uod/idr:/uod/idr:ro \ | |
-v "${IDR_WRITEABLE}:/scratch" \ | |
simleo/pyfeatures \ | |
serialize \ | |
"${IDR_METADATA}/${screen_file}" \ | |
-o "/scratch/out/${screen_name}" | |
done < "${IDR_METADATA}/${IDR_TSV}" |
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#!/bin/bash | |
set -eu | |
shopt -s nullglob | |
AVRO_PARENTDIR=/uod/idr/scratch/features-input-avro/idr0013-neumann-mitocheck/idr0013-neumann-mitocheck_screenA_ts-6-46-86 | |
IDR_WRITEABLE=/home/idr-scratch/spli | |
RUNAS_USER=11904 | |
ADD_TASK="../venv/bin/python tasks.py" | |
TASKID_LOG=taskid-calc.log | |
CALC_PARAMS="-l -W 672 -H 512 -x 672 -y 512" | |
RUN=0 | |
if [ "${1:-}" = "-run" ]; then | |
RUN=1 | |
fi | |
if [ ! -f tasks.py ]; then | |
echo "ERROR: Must be run from the celery-example directory" | |
exit 2 | |
fi | |
if [ -f "$TASKID_LOG" ]; then | |
echo "ERROR: \$TASKID_LOG=$TASKID_LOG already exists, delete or rename it" | |
exit 2 | |
fi | |
echoruntee() { | |
echo "$@" | |
if [ $RUN -eq 1 ]; then | |
"$@" | tee -a "$TASKID_LOG" | |
fi | |
} | |
count=0 | |
TESTING_LIMIT=0 | |
for parent in "$AVRO_PARENTDIR/"*/; do | |
for avro in "$parent"/*.avro; do | |
outdir="$(basename $parent)" | |
logbasename="$outdir/$(basename ${avro%.avro})" | |
count=$((count + 1)) | |
echoruntee $ADD_TASK \ | |
docker run --rm -u "$RUNAS_USER" \ | |
-v /uod/idr:/uod/idr:ro \ | |
-v "$IDR_WRITEABLE:/scratch" \ | |
manics/pyfeatures \ | |
--stdout "/scratch/out/$logbasename-out.log" \ | |
--stderr "/scratch/out/$logbasename-err.log" \ | |
calc \ | |
"$avro" \ | |
$CALC_PARAMS \ | |
-o "/scratch/out/$outdir" | |
# Use = so that we can easily disable by setting TESTING_LIMIT=0 | |
if [ "$TESTING_LIMIT" = "$count" ]; then | |
break 2 | |
fi | |
done | |
done |
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#!/bin/bash | |
set -eu | |
IDR_METADATA=/uod/idr/homes/scratch/spli/idr-metadata | |
IDR_TSV=idr0013-neumann-mitocheck/screenA/idr0013-screenA-plates.tsv | |
IDR_WRITEABLE=/home/idr-scratch/spli | |
RUNAS_USER=11904 | |
ADD_TASK="../venv/bin/python tasks.py" | |
TASKID_LOG=taskid-serialize.log | |
RUN=0 | |
if [ "${1:-}" = "-run" ]; then | |
RUN=1 | |
fi | |
if [ ! -f tasks.py ]; then | |
echo "ERROR: Must be run from the celery-example directory" | |
exit 2 | |
fi | |
if [ -f "$TASKID_LOG" ]; then | |
echo "ERROR: \$TASKID_LOG=$TASKID_LOG already exists, delete or rename it" | |
exit 2 | |
fi | |
echoruntee() { | |
echo "$@" | |
if [ $RUN -eq 1 ]; then | |
"$@" | tee -a "$TASKID_LOG" | |
fi | |
} | |
while IFS=$'\t' read -r -a arr; do | |
screen_name="${arr[0]}" | |
screen_file="${arr[1]}" | |
echoruntee $ADD_TASK \ | |
docker run --rm -u "$RUNAS_USER" \ | |
-v /uod/idr:/uod/idr:ro \ | |
-v "$IDR_WRITEABLE:/scratch" \ | |
manics/pyfeatures \ | |
--stdout "/scratch/out/$screen_name-out.log" \ | |
--stderr "/scratch/out/$screen_name-err.log" \ | |
serialize \ | |
"$IDR_METADATA/$screen_file" \ | |
-o "/scratch/out/$screen_name" \ | |
-ts 6,46,86 | |
done < "$IDR_METADATA/$IDR_TSV" |
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