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97
run_scripts/multi-sem/wafer-53/92_adjust_layer_intensity.sh
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,97 @@ | ||
| #!/bin/bash | ||
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| set -e | ||
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| ABSOLUTE_SCRIPT=`readlink -m $0` | ||
| SCRIPT_DIR=`dirname ${ABSOLUTE_SCRIPT}` | ||
| source ${SCRIPT_DIR}/00_config.sh | ||
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| umask 0002 | ||
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| if (( $# < 1 )); then | ||
| echo """ | ||
| USAGE: $0 <number of nodes> | ||
| """ | ||
| exit 1 | ||
| fi | ||
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| N_NODES="${1}" # normalizing a 10-slab volume with 180 11-slot workers took 2 hours and 15 minutes | ||
| NORMALIZE_METHOD="LOCAL_CONTRAST" | ||
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| SOURCE_DATASET="/wafer-53-align/run_20240410_173647/pass06" | ||
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| #----------------------------------------------------------- | ||
| NORMALIZED_LAYER_SUFFIX="_norm-layer" | ||
| NORMALIZED_LOCAL_SUFFIX="_norm-local" | ||
| if [[ "${NORMALIZE_METHOD}" == "LAYER_INTENSITY" ]]; then | ||
| NORMALIZED_SUFFIX="${NORMALIZED_LAYER_SUFFIX}" | ||
| elif [[ "${NORMALIZE_METHOD}" == "LOCAL_CONTRAST" ]]; then | ||
| NORMALIZED_SUFFIX="${NORMALIZED_LOCAL_SUFFIX}" | ||
| else | ||
| echo "ERROR: unknown NORMALIZE_METHOD of ${NORMALIZE_METHOD}" | ||
| exit 1 | ||
| fi | ||
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| NORMALIZED_SUFFIX="${NORMALIZED_SUFFIX}_inverted" | ||
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| SOURCE_PATH="${N5_SAMPLE_PATH}${SOURCE_DATASET}" | ||
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| if [[ ! -d ${SOURCE_PATH} ]]; then | ||
| echo "ERROR: ${SOURCE_PATH} not found" | ||
| exit 1 | ||
| fi | ||
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| #----------------------------------------------------------- | ||
| # Spark executor setup with 11 cores per worker ... | ||
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| export N_EXECUTORS_PER_NODE=2 # 6 | ||
| export N_CORES_PER_EXECUTOR=5 # 5 | ||
| # To distribute work evenly, recommended number of tasks/partitions is 3 times the number of cores. | ||
| #N_TASKS_PER_EXECUTOR_CORE=3 | ||
| export N_OVERHEAD_CORES_PER_WORKER=1 | ||
| #N_CORES_PER_WORKER=$(( (N_EXECUTORS_PER_NODE * N_CORES_PER_EXECUTOR) + N_OVERHEAD_CORES_PER_WORKER )) | ||
| export N_CORES_DRIVER=1 | ||
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| #----------------------------------------------------------- | ||
| RUN_TIME=`date +"%Y%m%d_%H%M%S"` | ||
| JAR="/groups/flyem/data/render/lib/hot-knife-0.0.5-SNAPSHOT.jar" | ||
| CLASS="org.janelia.saalfeldlab.hotknife.SparkNormalizeN5" | ||
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| # /nrs/hess/render/export/hess.n5/render/wafer_52_cut_00030_to_00039/slab_045_all_align_t2_ic___20230123_162917 | ||
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| ARGV="\ | ||
| --n5PathInput=${N5_SAMPLE_PATH} \ | ||
| --n5DatasetInput=${SOURCE_DATASET} \ | ||
| --normalizeMethod=${NORMALIZE_METHOD} \ | ||
| --factors=2,2,1 \ | ||
| --invert" | ||
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| NORMALIZED_DATASET="${SOURCE_DATASET}${NORMALIZED_SUFFIX}" | ||
| NORMALIZED_DATASET_DIR="${N5_SAMPLE_PATH}${NORMALIZED_DATASET}" | ||
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| if [[ ! -d ${NORMALIZED_DATASET_DIR} ]]; then | ||
| mkdir -p "${NORMALIZED_DATASET_DIR}" | ||
| if [[ -f ${SOURCE_PATH}/attributes.json ]]; then | ||
| cp "${SOURCE_PATH}"/attributes.json "${NORMALIZED_DATASET_DIR}" | ||
| echo "copied ${SOURCE_PATH}/attributes.json to ${N5_SAMPLE_PATH}${NORMALIZED_DATASET}" | ||
| fi | ||
| fi | ||
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| LOG_DIR="logs" | ||
| LOG_FILE="${LOG_DIR}/norm.${RUN_TIME}.out" | ||
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| mkdir -p ${LOG_DIR} | ||
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| # use shell group to tee all output to log file | ||
| { | ||
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| echo "Running with arguments: | ||
| ${ARGV} | ||
| " | ||
| /groups/flyTEM/flyTEM/render/spark/spark-janelia/flintstone.sh $N_NODES $JAR $CLASS $ARGV | ||
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| echo "normalized n5 volume is: | ||
| -i ${N5_SAMPLE_PATH} -d ${NORMALIZED_DATASET} | ||
| " | ||
| } 2>&1 | tee -a ${LOG_FILE} | ||
|
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