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test_pipeline.sh
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test_pipeline.sh
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# -----------------------------------------------------#
#Process LUNA for retraining
# -----------------------------------------------------#
python3.4 dsb3.py 0 -s '' -ds 'LUNA16'
python3.4 dsb3.py 2 -s '' -ds 'LUNA16'
python3.4 dsb3.py 6 -s '' -ds 'LUNA16' #(bug) always uses entire data, will fail if previous steps use 10 patients
#Train Segmentation
cd ../dsb3_networks/nodule_segmentation/net/
python3.4 run.py stage1
python3.4 run.py stage2
# copy checkpoint to nodule segmentation
cp -r output_dir/128x128_5Channels_mutliview_stage2 ../../../checkpoints/nodule_segmentation
cd ../../../dsb3a/
python3.4 dsb3.py 1 -s '' -ds 'LUNA16'
python3.4 dsb3.py 3 -s '' -ds 'LUNA16'
python3.4 dsb3.py 4 -s '' -ds 'LUNA16'
#binaries luna candidate_lists
python3.4 binarize_candidates.py
#Train noduleness classifier
cd ../dsb3_networks/classification/luna_resnet2D/
python3.4 run.py
cd ../luna_resnet3D/
python3.4 run.py
cd ../../../dsb3a/
# -----------------------------------------------------#
#Run dsb3 processing / model training
# -----------------------------------------------------#
python3.4 dsb3.py 0 -s ''
python3.4 dsb3.py 1 -s ''
python3.4 dsb3.py 3 -s ''
#make links
cd ../datapipeline_final/dsb3_0/
ln -s gen_candidates gen_candidates_res05
ln -s gen_candidates gen_candidates_res07
ln -s resample_lungs resample_lungs_res05
ln -s resample_lungs resample_lungs_res07
cd ../../dsb3a/
python3.4 dsb3.py 4 -s '_res05'
python3.4 dsb3.py 4 -s '_res07'
python3.4 enforce_ordering.py
#100 - 0 split
cd ../dsb3_networks/classification/resnet2D_0.5res_100/
python3.4 run.py
cd ../resnet2D_0.7res_100/
python3.4 run.py
cd ../resnet3D_0.5res_100/
python3.4 run.py
cd ../resnet3D_0.7res_100/
python3.4 run.py
#80 - 20 split
cd ../resnet2D_0.5res_80/
python3.4 run.py
cd ../resnet3D_0.5res_80/
python3.4 run.py
cd ../resnet2D_0.7res_80/
python3.4 run.py
cd ../resnet3D_0.7res_80/
python3.4 run.py
cd ../../../dsb3a/
#sub 1
python3.4 dsb3.py 7 -s '_2D_05res_80'
python3.4 dsb3.py 7 -s '_2D_07res_80'
python3.4 dsb3.py 7 -s '_3D_05res_80'
python3.4 dsb3.py 7 -s '_3D_07res_80'
#sub 2
python3.4 dsb3.py 7 -s '_2D_05res_100'
python3.4 dsb3.py 7 -s '_2D_07res_100'
python3.4 dsb3.py 7 -s '_3D_05res_100'
python3.4 dsb3.py 7 -s '_3D_07res_100'
#combine submissions (average)
python3.4 combine_subs.py