-
Notifications
You must be signed in to change notification settings - Fork 1
/
tiling.sh
28 lines (26 loc) · 980 Bytes
/
tiling.sh
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
#!/bin/bash
#SBATCH --job-name=augmented
#SBATCH --array=0-4%5
#SBATCH --partition=gpu
#SBATCH --cpus-per-task=8
#SBATCH --gres=gpu:1
#SBATCH --ntasks=1
#SBATCH --ntasks-per-node=1
#SBATCH --hint=nomultithread
#SBATCH --time=03:00:00
#SBATCH --output=tiling_%x.out
#SBATCH --error=tiling_%x.out
tiler_type='SharedAugTiler'
path_wsi="./test_dataset/slides"
ext='svs'
path_outputs="./test_dataset/encoded"
model_path="/path/of/the/model/if/using/ssl/for/encoding.pth"
level=1
size=224
tiler="imagenet"
normalizer="macenko"
Naug=50
Nt=256
NWSI=10 # Number of WSI per job. set the array so that NWSI * Njobs = total number of WSI
num_worker=8 #Set it as the number of cpus per task
python build_dataset/main_tiling.py --path_wsi "$path_wsi" --ext $ext --level "$level" --tiler "$tiler" --size "$size" --model_path "$model_path" --path_outputs "$path_outputs" --normalizer "$normalizer" --Naug $Naug --Nt $Nt --NWSI $NWSI --tiler_type $tiler_type