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add 3dunet model #811

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merged 26 commits into from
May 29, 2023
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18ebfdf
add 3dunet model
violetch24 Apr 18, 2023
e29877e
remove extra files
violetch24 Apr 19, 2023
15038e4
minor fix
violetch24 Apr 19, 2023
fc4156b
Merge branch 'master' into zixuan/3dunet
violetch24 Apr 19, 2023
73c8e26
Merge branch 'master' into zixuan/3dunet
violetch24 Apr 20, 2023
f7375ff
edit requirements.txt
violetch24 Apr 20, 2023
e510a7a
minor fix
violetch24 Apr 20, 2023
55e0b32
Merge branch 'master' into zixuan/3dunet
violetch24 Apr 20, 2023
6e2339f
edit requirements.txt
violetch24 Apr 20, 2023
f21ca15
Merge branch 'master' into zixuan/3dunet
violetch24 Apr 26, 2023
77bc2af
replace sklearn
violetch24 Apr 26, 2023
100fa36
minor fix
violetch24 Apr 26, 2023
719444a
Merge branch 'master' into zixuan/3dunet
violetch24 Apr 28, 2023
459c4ed
Merge branch 'master' into zixuan/3dunet
violetch24 May 8, 2023
fc85247
Merge branch 'master' into zixuan/3dunet
violetch24 May 10, 2023
60302cf
Merge branch 'master' into zixuan/3dunet
violetch24 May 17, 2023
0d9752c
Merge branch 'master' into zixuan/3dunet
violetch24 May 18, 2023
284c77e
fix for int8 accuracy
violetch24 May 18, 2023
c389934
Merge branch 'master' into zixuan/3dunet
violetch24 May 19, 2023
8733e99
minor fix
violetch24 May 19, 2023
babd06d
Merge branch 'master' into zixuan/3dunet
violetch24 May 19, 2023
008b13b
minor fix
violetch24 May 19, 2023
1113b8f
Merge branch 'master' into zixuan/3dunet
violetch24 May 22, 2023
c17c5c8
Merge branch 'master' into zixuan/3dunet
violetch24 May 22, 2023
44f2579
fix multiple instance issue
violetch24 May 22, 2023
d879176
minor fix
violetch24 May 23, 2023
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minor fix
Signed-off-by: Cheng, Zixuan <zixuan.cheng@intel.com>
violetch24 committed Apr 26, 2023
commit 100fa367f3184f2326f6519b8cc0186c5a519ae4
Original file line number Diff line number Diff line change
@@ -23,6 +23,8 @@ pip install -r requirements.txt
# install dependency required by data preprocessing script
git clone https://github.com/MIC-DKFZ/nnUNet.git --recursive
cd nnUNet/
# replace sklearn in the older version with scikit-learn
sed -i 's/sklearn/scikit-learn/g' setup.py
git checkout b38c69b345b2f60cd0d053039669e8f988b0c0af
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python setup.py install
cd ..
Original file line number Diff line number Diff line change
@@ -52,7 +52,6 @@ function init_params {

# run_benchmark
function run_benchmark {
sed -i 's/sklearn/scikit-learn/g' ./nnUNet/setup.py
if [[ ${int8} == "true" ]]; then
extra_cmd="--int8"
else
Original file line number Diff line number Diff line change
@@ -37,7 +37,6 @@ function init_params {

# run_tuning
function run_tuning {
sed -i 's/sklearn/scikit-learn/g' ./nnUNet/setup.py
python run.py \
--model_dir=${input_model} \
--backend=pytorch --accuracy \