scripts/convert_all.sh

#!/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