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commands.txt
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commands.txt
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### To run the simulation
```
run-mc --data-folder /mnt/nas_io/anarchy/4d_cbct_mc/4d_ct_lung_uke_artifact_free --output-folder /mnt/nas_io/anarchy/4d_cbct_mc/speedup --reference --speedups 2 --speedups 5 --speedups 10 --phases 0 --segmenter-weights /mnt/nas_io/anarchy/4d_cbct_mc/segmenter/2023-09-21T17:18:03.218908_run_39a7956b4719411f99ddf071__step_95000.pth --segmenter-patch-overlap 0.75 --reconstruct --gpu 0 --gpu 1
```
run-mc --data-folder /datalake_fast/4d_ct_lung_uke_artifact_free --output-folder /datalake_fast/mc_output/3d --phases 0 --gpu 0 --reference --regex 024.* --n-projections 90
run-mc --data-folder /datalake_fast/4d_ct_lung_uke_artifact_free --output-folder /datalake_fast/mc_output/3d --phases 0 --gpu 0 --reference --regex 024.* --segmenter-weights /mnt/nas_io/anarchy/4d_cbct_mc/segmenter/2023-09-21T17:18:03.218908_run_39a7956b4719411f99ddf071__step_95000.pth --segmenter-patch-overlap 0.25 --segmenter-patch-shape 128 128 128
run-mc --data-folder /datalake_fast/4d_ct_lung_uke_artifact_free --output-folder /datalake_fast/mc_output/4d --phases 0 --gpu 0 --reference --regex 024.* --correspondence-model /mnt/nas_io/anarchy/4d_cbct_mc/024_correspondence_model.pkl --respiratory-signal /mnt/nas_io/anarchy/4d_cbct_mc/024_respiratory_signal.pkl
run-mc --data-folder /datalake_fast/4d_ct_lung_uke_artifact_free --output-folder /datalake_fast/mc_output/4d --phases 0 --gpu 0 --reference --regex 024.* --segmenter-weights /mnt/nas_io/anarchy/4d_cbct_mc/segmenter/2023-09-21T17:18:03.218908_run_39a7956b4719411f99ddf071__step_95000.pth --segmenter-patch-overlap 0.25 --segmenter-patch-shape 496 496 32 --correspondence-model /mnt/nas_io/anarchy/4d_cbct_mc/024_correspondence_model.pkl --respiratory-signal /mnt/nas_io/anarchy/4d_cbct_mc/024_respiratory_signal.pkl
run-mc --data-folder /mnt/nas_io/anarchy/4d_cbct_mc/4d_ct_lung_uke_artifact_free --output-folder /mnt/nas_io/anarchy/4d_cbct_mc/speedup --phases 0 --gpu 0 --gpu 1 --gpu 2 --gpu 4 --gpu 5 --speedups 20 --speedups 50 --regex 024.* --forward-projection --reconstruct
run-mc --data-folder /data_l79a/fmadesta/4d_cbct/R4DCIRS/4DCT --output-folder /datalake_fast/mc_output/4d_cirs --phases 2 --gpu 0 --speedups 10 --regex phase_based_gt_curve --segmenter-weights /mnt/nas_io/anarchy/4d_cbct_mc/segmenter/2023-09-21T17:18:03.218908_run_39a7956b4719411f99ddf071__step_95000.pth --segmenter-patch-overlap 0.25 --segmenter-patch-shape 288 288 32 --correspondence-model /mnt/nas_io/anarchy/4d_cbct_mc/cirs_correspondence_model.pkl --respiratory-signal /mnt/nas_io/anarchy/4d_cbct_mc/cirs_varian_respiratory_signal.pkl --respiratory-signal-quantization 20 --cirs-phantom --reconstruct
run-mc --output-folder /datalake_fast/mc_output/4d_cirs --phases 2 --gpu 1 --reference --geometry-filepath /data_l79a/fmadesta/4d_cbct/R4DCIRS/for_mc/4d_cirs/cirs_phase_02.pkl --correspondence-model /data_l79a/fmadesta/4d_cbct/R4DCIRS/for_mc/4d_cirs/cirs_correspondence_model.pkl --respiratory-signal /data_l79a/fmadesta/4d_cbct/R4DCIRS/for_mc/4d_cirs/cirs_varian_respiratory_signal.pkl --respiratory-signal-quantization 40 --cirs-phantom --reconstruct
CatPhan runs:
run-mc --output-folder /mnt/nas_io/anarchy/4d_cbct_mc/catphan --gpu 0 --gpu 1 --gpu 2 --reference --speedups 10.0 --speedups 20.0 --speedups 50.0 --catphan-phantom --reconstruct
4D CIRS runs:
run-mc --output-folder /datalake_fast/mc_output/4d_cirs --phases 2 --gpu 1 --gpu 0 --reference --geometry-filepath /data_l79a/fmadesta/4d_cbct/R4DCIRS/for_mc/4d_cirs/cirs_phase_02.pkl --correspondence-model /data_l79a/fmadesta/4d_cbct/R4DCIRS/for_mc/4d_cirs/cirs_correspondence_model.pkl --respiratory-signal /data_l79a/fmadesta/4d_cbct/R4DCIRS/for_mc/4d_cirs/cirs_varian_respiratory_signal.pkl --respiratory-signal-quantization 20 --cirs-phantom --reconstruct --forward-projection
run-mc --output-folder /datalake_fast/mc_output/4d_cirs --phases 2 --gpu 1 --gpu 0 --speedups 20 --geometry-filepath /data_l79a/fmadesta/4d_cbct/R4DCIRS/for_mc/4d_cirs_large/cirs_phase_02.pkl --correspondence-model /data_l79a/fmadesta/4d_cbct/R4DCIRS/for_mc/4d_cirs_large/cirs_correspondence_model.pkl --respiratory-signal /data_l79a/fmadesta/4d_cbct/R4DCIRS/for_mc/4d_cirs_large/cirs_varian_respiratory_signal.pkl --respiratory-signal-quantization 20 --cirs-phantom --reconstruct --forward-projection
run-mc --output-folder /mnt/nas_io/anarchy/4d_cbct_mc/4d/cirs/output --phases 2 --gpu 0 --gpu 1 --gpu 2 --reference --speedups 50 --geometry-filepath /mnt/nas_io/anarchy/4d_cbct_mc/4d/cirs/for_mc/4d_cirs_large_with_water/cirs_phase_02.pkl --correspondence-model /mnt/nas_io/anarchy/4d_cbct_mc/4d/cirs/for_mc/4d_cirs_large_with_water/cirs_correspondence_model.pkl --respiratory-signal /mnt/nas_io/anarchy/4d_cbct_mc/4d/cirs/for_mc/4d_cirs_large_with_water/cirs_varian_respiratory_signal.pkl --respiratory-signal-quantization 20 --cirs-phantom --reconstruct --forward-projection
4D patient runs:
run-mc --data-folder /mnt/nas_io/anarchy/4d_cbct_mc/4d_ct_lung_uke_artifact_free --output-folder /mnt/nas_io/anarchy/4d_cbct_mc/4d --phases 2 --gpu 0 --gpu 1 --gpu 2 --gpu 4 --gpu 5 --reference --speedups 20 --speedups 10 --regex 024.* --correspondence-model /mnt/nas_io/anarchy/4d_cbct_mc/024_correspondence_model_nonmasked.pkl --respiratory-signal /mnt/nas_io/anarchy/4d_cbct_mc/024_respiratory_signal.pkl --segmenter-weights /mnt/nas_io/anarchy/4d_cbct_mc/segmenter/2023-09-21T17:18:03.218908_run_39a7956b4719411f99ddf071__step_95000.pth --reconstruct --forward-projection --respiratory-signal-quantization 20
run-mc --data-folder /mnt/nas_io/anarchy/4d_cbct_mc/4d_ct_lung_uke_artifact_free --output-folder /mnt/nas_io/anarchy/4d_cbct_mc/4d_2 --phases 2 --gpu 1 --gpu 0 --speedups 20 --speedups 10 --regex 024.* --correspondence-model /mnt/nas_io/anarchy/4d_cbct_mc/024_correspondence_model_nonmasked.pkl --respiratory-signal /mnt/nas_io/anarchy/4d_cbct_mc/024_respiratory_signal.pkl --segmenter-weights /mnt/nas_io/anarchy/4d_cbct_mc/segmenter/2023-09-21T17:18:03.218908_run_39a7956b4719411f99ddf071__step_95000.pth --reconstruct --forward-projection --respiratory-signal-quantization 20
run-mc --data-folder /mnt/nas_io/anarchy/4d_cbct_mc/4d/R2017025 --output-folder /mnt/nas_io/anarchy/4d_cbct_mc/4d/R2017025/mc --phases 2 --gpu 5 --gpu 0 --gpu 1 --gpu 2 --gpu 4 --reference --speedups 20 --speedups 10 --regex ct_rai* --correspondence-model /mnt/nas_io/anarchy/4d_cbct_mc/4d/R2017025/correspondence_model_rai.pkl --respiratory-signal /mnt/nas_io/anarchy/4d_cbct_mc/4d/R2017025/cbct_respiratory_signal.pkl --segmenter-weights /mnt/nas_io/anarchy/4d_cbct_mc/segmenter/2023-09-21T17:18:03.218908_run_39a7956b4719411f99ddf071__step_95000.pth --reconstruct --forward-projection --respiratory-signal-quantization 20
run-mc --data-folder /mnt/nas_io/anarchy/4d_cbct_mc/4d/R2017025 --output-folder /mnt/nas_io/anarchy/4d_cbct_mc/4d/R2017025/mc --phases 2 --gpu 0 --gpu 1 --gpu 2 --speedups 20 --regex ct_rai* --correspondence-model /mnt/nas_io/anarchy/4d_cbct_mc/4d/R2017025/correspondence_model_rai.pkl --respiratory-signal /mnt/nas_io/anarchy/4d_cbct_mc/4d/R2017025/cbct_respiratory_signal.pkl --segmenter-weights /mnt/nas_io/anarchy/4d_cbct_mc/segmenter/2023-09-21T17:18:03.218908_run_39a7956b4719411f99ddf071__step_95000.pth --reconstruct --forward-projection --respiratory-signal-quantization 20
run-mc --image-filepath /mnt/nas_io/anarchy/4d_cbct_mc/4d/R2017025/ct_rai/bin_02.nii --output-folder /mnt/nas_io/anarchy/4d_cbct_mc/3d/R2017025 --gpu 1 --speedups 50 --segmenter-weights /mnt/nas_io/anarchy/4d_cbct_mc/segmenter/2023-09-21T17:18:03.218908_run_39a7956b4719411f99ddf071__step_95000.pth --reconstruct-3d --forward-projection --speedup-weights /datalake3/speedup_runs_all_speedups/2024-01-17T18:17:39.555467_run_f28354c2c6484ce5a7b5a783/models/training/step_20000.pth
debug: run-mc --data-folder /mnt/nas_io/anarchy/4d_cbct_mc/4d/R2017025 --output-folder /mnt/nas_io/anarchy/4d_cbct_mc/4d/R2017025/mc/debug --phases 2 --gpu 1 --gpu 0 --reference --regex ct_rai* --correspondence-model /mnt/nas_io/anarchy/4d_cbct_mc/4d/R2017025/correspondence_model.pkl --respiratory-signal /mnt/nas_io/anarchy/4d_cbct_mc/4d/R2017025/cbct_respiratory_signal.pkl --segmenter-weights /mnt/nas_io/anarchy/4d_cbct_mc/segmenter/2023-09-21T17:18:03.218908_run_39a7956b4719411f99ddf071__step_95000.pth --reconstruct --forward-projection --n-projections 1 --respiratory-signal-quantization 20