Datasets:
File size: 2,155 Bytes
7216554 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 | #!/bin/bash
#SBATCH --job-name=conv_all
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --mem=128G
#SBATCH --time=12:00:00
#SBATCH --output=logs/convert_all_%j.out
#SBATCH --error=logs/convert_all_%j.err
echo "=== Converting All Datasets at $(date) ==="
source /dgx1data/res/azradonc/m338067/miniconda3/etc/profile.d/conda.sh
conda activate biomedparse
cd /dgx1data/res/azradonc/m338067/BiomedParse/OmniTumorData
# BraTS (Brain MRI)
echo ""
echo "=== Converting BraTS ==="
python3 convert_fast.py --input brats --output brats_png --workers 32 --dataset brats
# COVID-19 CT
echo ""
echo "=== Converting COVID-19 CT ==="
python3 convert_fast.py --input covid19_ct --output covid19_ct_png --workers 32 --dataset covid19_ct
# MSD Tasks
echo ""
echo "=== Converting MSD_Task01_BrainTumour ==="
python3 convert_fast.py --input MSD_Task01_BrainTumour --output MSD_Task01_png --workers 32 --dataset MSD_Task01_BrainTumour
echo ""
echo "=== Converting MSD_Task05_Prostate ==="
python3 convert_fast.py --input MSD_Task05_Prostate --output MSD_Task05_png --workers 32 --dataset MSD_Task05_Prostate
echo ""
echo "=== Converting MSD_Task08_HepaticVessel ==="
python3 convert_fast.py --input MSD_Task08_HepaticVessel --output MSD_Task08_png --workers 32 --dataset MSD_Task08_HepaticVessel
# ULS23 Part1 (Novel data)
echo ""
echo "=== Converting ULS23 Part1 ==="
python3 convert_fast.py --input uls23_part1 --output uls23_part1_png --workers 32 --dataset uls23_part1
# ULS23 Part2 (Fully annotated)
echo ""
echo "=== Converting ULS23 Part2 ==="
python3 convert_fast.py --input uls23_part2 --output uls23_part2_png --workers 32 --dataset uls23_part2
# ULS23 Part3 (Fully + Partially annotated)
echo ""
echo "=== Converting ULS23 Part3 ==="
python3 convert_fast.py --input uls23_part3 --output uls23_part3_png --workers 32 --dataset uls23_part3
echo ""
echo "=== All Done at $(date) ==="
# Summary
echo ""
echo "=== Summary ==="
for d in *_png; do
if [ -d "$d" ]; then
cnt=$(find "$d/images" -name '*.png' 2>/dev/null | wc -l)
sz=$(du -sh "$d" 2>/dev/null | cut -f1)
echo "$d: $cnt images, $sz"
fi
done
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