OpenScientificCodeRegistry/Database

1{2 "format": "oscr-script-manifest/1",3 "repository": "github.com/mic-dkfz/nnunet",4 "url": "https://github.com/MIC-DKFZ/nnUNet/tree/master",5 "host": "github.com",6 "commit": "202f6baa0adc2ef5f7b615df19cc4da970412cc0",7 "license": "Apache-2.0",8 "license_confirmed_by": "license file LICENSE",9 "redistribution": "yes",10 "files": [11  {12   "path": ".github/scripts/safe-label.sh",13   "sha256": "4d884fcf72cc20ff00160682124462c00970c030a4093aed45b60bf26c38c90e",14   "language": "Shell",15   "lines": 46,16   "truncated": false,17   "block": 1,18   "row": 1162419  },20  {21   "path": ".github/scripts/safe-pr-review.sh",22   "sha256": "6c438133e4e13a65473063197c38aa9be503f0cac35fb44a94e0fd7c9275b41e",23   "language": "Shell",24   "lines": 29,25   "truncated": false,26   "block": 1,27   "row": 1148628  },29  {30   "path": "LICENSE",31   "sha256": "ff93b6fdf1d59f7c48ca7f44f2d0db47bb7743a1c6fa0f4c5f4d7809f78ce70e",32   "language": "License",33   "lines": 201,34   "truncated": false,35   "block": 1,36   "row": 221937  },38  {39   "path": "documentation/competitions/FLARE24/Task_1/inference_flare_task1.py",40   "sha256": "d8697fc7454fc4c9b4ecc59b380de36242c3319dfe0ead1bef47666be628ee11",41   "language": "Python",42   "lines": 209,43   "truncated": false,44   "block": 1,45   "row": 864946  },47  {48   "path": "documentation/competitions/FLARE24/Task_2/inference_flare_task2.py",49   "sha256": "84dc15e740e27cd50c79a7fb004476db96db0842d557a8f2add6acfcb4182896",50   "language": "Python",51   "lines": 467,52   "truncated": false,53   "block": 1,54   "row": 947955  },56  {57   "path": "documentation/competitions/Toothfairy2/inference_script_semseg_only_customInf2.py",58   "sha256": "bf1d0375d5a082b041cf060ef74f520baccd30b297ea2075cab3426d87e40c98",59   "language": "Python",60   "lines": 359,61   "truncated": false,62   "block": 1,63   "row": 907364  },65  {66   "path": "nnunetv2/batch_running/benchmarking/generate_benchmarking_commands.py",67   "sha256": "3ba3831200199c7626daa229c369d7b9de265731b626beb111414ce6c41a72ea",68   "language": "Python",69   "lines": 41,70   "truncated": false,71   "block": 1,72   "row": 630073  },74  {75   "path": "nnunetv2/batch_running/benchmarking/summarize_benchmark_results.py",76   "sha256": "c48b27489bc8a3e46d07eb3b516e917f3af595e8b8bfddf20c5f6da8341c766a",77   "language": "Python",78   "lines": 69,79   "truncated": false,80   "block": 1,81   "row": 687782  },83  {84   "path": "nnunetv2/batch_running/collect_results_custom_Decathlon.py",85   "sha256": "56f21676a0d7ece3ff18be9c9c504c5b840d726191e34e422065fa8a7d7601c2",86   "language": "Python",87   "lines": 121,88   "truncated": false,89   "block": 1,90   "row": 771291  },92  {93   "path": "nnunetv2/batch_running/collect_results_custom_Decathlon_2d.py",94   "sha256": "48089272883a32133deb5c0aa0b1fa99ac261a8e3d5ab9479bc55158877c4c6a",95   "language": "Python",96   "lines": 17,97   "truncated": false,98   "block": 1,99   "row": 5524100  },101  {102   "path": "nnunetv2/batch_running/generate_lsf_runs_customDecathlon.py",103   "sha256": "12e895f38f77604ebabebcb6713d6f7fbb27d591beb056bffb634a22cd2ad58d",104   "language": "Python",105   "lines": 111,106   "truncated": false,107   "block": 1,108   "row": 7438109  },110  {111   "path": "nnunetv2/batch_running/jobs.sh",112   "sha256": "b305a09b3d486e3489e2b9f88a880dd406ac6242efd90302788d0f5d28668449",113   "language": "Shell",114   "lines": 52,115   "truncated": false,116   "block": 1,117   "row": 11744118  },119  {120   "path": "nnunetv2/batch_running/release_trainings/nnunetv2_v1/collect_results.py",121   "sha256": "ffc6b25b33e94b1ee35544ea6dcf51939111c596625c8c7529cd0d5b8639e788",122   "language": "Python",123   "lines": 112,124   "truncated": false,125   "block": 1,126   "row": 7618127  },128  {129   "path": "nnunetv2/batch_running/release_trainings/nnunetv2_v1/generate_lsf_commands.py",130   "sha256": "270310f73c8b80187b1e48eb4164f0aa5df9a9e4cc3d1e92b7a4c472f5124ac4",131   "language": "Python",132   "lines": 91,133   "truncated": false,134   "block": 1,135   "row": 7069136  },137  {138   "path": "nnunetv2/configuration.py",139   "sha256": "c62f73b1bc1111b0bc9c3dfe5c8d1a481047bbb2c128b6017ede97da2af17beb",140   "language": "Python",141   "lines": 10,142   "truncated": false,143   "block": 1,144   "row": 5326145  },146  {147   "path": "nnunetv2/dataset_conversion/Dataset015_018_RibFrac_RibSeg.py",148   "sha256": "6021689ae577f8e002f8b10b9e11fb72d457215376cabc0d71f61821201cc333",149   "language": "Python",150   "lines": 147,151   "truncated": false,152   "block": 1,153   "row": 7580154  },155  {156   "path": "nnunetv2/dataset_conversion/Dataset021_CTAAorta.py",157   "sha256": "b6f0488a2f244227219049232877cc19dc3d8e2b44f32cef6a8cb1e44e7d1c6f",158   "language": "Python",159   "lines": 70,160   "truncated": false,161   "block": 1,162   "row": 6451163  },164  {165   "path": "nnunetv2/dataset_conversion/Dataset023_AbdomenAtlas1_1Mini.py",166   "sha256": "bb34fc440e4a3143e512ae061161fe3c780aa190beed8c46fb1c1d2b1fbfc352",167   "language": "Python",168   "lines": 55,169   "truncated": false,170   "block": 1,171   "row": 6475172  },173  {174   "path": "nnunetv2/dataset_conversion/Dataset027_ACDC.py",175   "sha256": "833c9bbbb0fe3355e550368a8af1d0340058852e91de44f13d9e72b5886436b0",176   "language": "Python",177   "lines": 114,178   "truncated": false,179   "block": 1,180   "row": 7309181  },182  {183   "path": "nnunetv2/dataset_conversion/Dataset042_BraTS18.py",184   "sha256": "a69dd8c0a5737ca3f6127f5c608373d9855e86cb18606af8d7e4822f8ee4dc59",185   "language": "Python",186   "lines": 110,187   "truncated": false,188   "block": 1,189   "row": 7385190  },191  {192   "path": "nnunetv2/dataset_conversion/Dataset043_BraTS19.py",193   "sha256": "adb330e9aaa079cf0ff23e398f4b59b712b158b9725acfa4f2f2f2751f6a5587",194   "language": "Python",195   "lines": 110,196   "truncated": false,197   "block": 1,198   "row": 7386199  },200  {201   "path": "nnunetv2/dataset_conversion/Dataset073_Fluo_C3DH_A549_SIM.py",202   "sha256": "ff615ff7b67226d925875985493b9eaba20939bd9651544bd508d62d37c5264b",203   "language": "Python",204   "lines": 84,205   "truncated": false,206   "block": 1,207   "row": 7193208  },209  {210   "path": "nnunetv2/dataset_conversion/Dataset114_MNMs.py",211   "sha256": "d1ac40e1583274cadf1b88d6899c402f01b08c61fec214d508347cb2bd2807a5",212   "language": "Python",213   "lines": 198,214   "truncated": false,215   "block": 1,216   "row": 8362217  },218  {219   "path": "nnunetv2/dataset_conversion/Dataset115_EMIDEC.py",220   "sha256": "41209b45ce2ec0576e172029c5a43287af31475d40efe4b8cb149e0cb77b0089",221   "language": "Python",222   "lines": 61,223   "truncated": false,224   "block": 1,225   "row": 6474226  },227  {228   "path": "nnunetv2/dataset_conversion/Dataset119_ToothFairy2_All.py",229   "sha256": "0c35ff5a280d3356b93e19aa41e439f21d961073feedf9d7fa87c25ead7426e6",230   "language": "Python",231   "lines": 196,232   "truncated": false,233   "block": 1,234   "row": 7898235  },236  {237   "path": "nnunetv2/dataset_conversion/Dataset120_RoadSegmentation.py",238   "sha256": "4551cbaa5af87580238c7b28f3ddaa551043d782bcca350041a10dad7dd8b713",239   "language": "Python",240   "lines": 86,241   "truncated": false,242   "block": 1,243   "row": 6932244  },245  {246   "path": "nnunetv2/dataset_conversion/Dataset137_BraTS21.py",247   "sha256": "bf26185c147961eeca20f03f7c4a358cf5eb44b678c19bb8bf7cc17164b08085",248   "language": "Python",249   "lines": 97,250   "truncated": false,251   "block": 1,252   "row": 7118253  },254  {255   "path": "nnunetv2/dataset_conversion/Dataset218_Amos2022_task1.py",256   "sha256": "18b0e6d5dc74aeeabca0960f089f2e6e8308d0eea3403d44378054102df23d44",257   "language": "Python",258   "lines": 68,259   "truncated": false,260   "block": 1,261   "row": 7041262  },263  {264   "path": "nnunetv2/dataset_conversion/Dataset219_Amos2022_task2.py",265   "sha256": "a41b0f369cf8f2b9cab2414b7faecc9bd022416e443ac83ba82036012cac136a",266   "language": "Python",267   "lines": 64,268   "truncated": false,269   "block": 1,270   "row": 6986271  },272  {273   "path": "nnunetv2/dataset_conversion/Dataset220_KiTS2023.py",274   "sha256": "f97256147a2563e22f831dcfa503c2f6a95785f722511b9fae590d19363b6c85",275   "language": "Python",276   "lines": 49,277   "truncated": false,278   "block": 1,279   "row": 6320280  },281  {282   "path": "nnunetv2/dataset_conversion/Dataset221_AutoPETII_2023.py",283   "sha256": "adb24656233a4ac01c0a7398076c2c8df43082b69e1facb1c1cce923476affe5",284   "language": "Python",285   "lines": 70,286   "truncated": false,287   "block": 1,288   "row": 6838289  },290  {291   "path": "nnunetv2/dataset_conversion/Dataset223_AMOS2022postChallenge.py",292   "sha256": "6c1b541a62b5be4b948e0f4874245610e6a5b76659df60558890efb339c10d1c",293   "language": "Python",294   "lines": 59,295   "truncated": false,296   "block": 1,297   "row": 6606298  },299  {300   "path": "nnunetv2/dataset_conversion/Dataset224_AbdomenAtlas1.0.py",301   "sha256": "f83032e393f718a46ba90c6a364994f92b8cd3a5bf9131459a0bb9cc28effae3",302   "language": "Python",303   "lines": 60,304   "truncated": false,305   "block": 1,306   "row": 6458307  },308  {309   "path": "nnunetv2/dataset_conversion/Dataset226_BraTS2024-BraTS-GLI.py",310   "sha256": "fe8228b892a1f647db3674f388f545c3c0cf6016c8ca5c1e0aeaa15b0b387847",311   "language": "Python",312   "lines": 55,313   "truncated": false,314   "block": 1,315   "row": 6367316  },317  {318   "path": "nnunetv2/dataset_conversion/Dataset227_TotalSegmentatorMRI.py",319   "sha256": "d5b21485ec81fd445ec7643ae5086688477f8f8d5d316bc07083d330804a1b94",320   "language": "Python",321   "lines": 54,322   "truncated": false,323   "block": 1,324   "row": 6377325  },326  {327   "path": "nnunetv2/dataset_conversion/Dataset987_dummyDataset4.py",328   "sha256": "b6a2fbe51d9007d0917cac4ce6da87dd0850798052a94798d8c82335c8befe11",329   "language": "Python",330   "lines": 32,331   "truncated": false,332   "block": 1,333   "row": 5937334  },335  {336   "path": "nnunetv2/dataset_conversion/Dataset989_dummyDataset4_2.py",337   "sha256": "3eec6f0bc34a6bb7e83d6ba96ffe4cdd06410d0bf9a8facbcf282a5303203711",338   "language": "Python",339   "lines": 32,340   "truncated": false,341   "block": 1,342   "row": 5955343  },344  {345   "path": "nnunetv2/dataset_conversion/convert_MSD_dataset.py",346   "sha256": "79ba852dfc114290eb9ec6c4ff376dac7d1d966f003f538f79ce20ddd13eba9a",347   "language": "Python",348   "lines": 131,349   "truncated": false,350   "block": 1,351   "row": 7717352  },353  {354   "path": "nnunetv2/dataset_conversion/convert_raw_dataset_from_old_nnunet_format.py",355   "sha256": "a007dc0cf6d3e383e9fbc0ad300e7a0b45ce95711ac969ec06f847699bb1cda6",356   "language": "Python",357   "lines": 53,358   "truncated": false,359   "block": 1,360   "row": 6722361  },362  {363   "path": "nnunetv2/dataset_conversion/datasets_for_integration_tests/Dataset996_IntegrationTest_Hippocampus_regions_ignore.py",364   "sha256": "85549973dbb0afff3327871a4cff191283626dcdfb472df3cc7486334968c722",365   "language": "Python",366   "lines": 73,367   "truncated": false,368   "block": 1,369   "row": 6827370  },371  {372   "path": "nnunetv2/dataset_conversion/datasets_for_integration_tests/Dataset997_IntegrationTest_Hippocampus_regions.py",373   "sha256": "0fdc2e99d835b33d8db1f8992a13d60619a587cd2f1b3230f1fea2d0e478f0da",374   "language": "Python",375   "lines": 37,376   "truncated": false,377   "block": 1,378   "row": 5988379  },380  {381   "path": "nnunetv2/dataset_conversion/datasets_for_integration_tests/Dataset998_IntegrationTest_Hippocampus_ignore.py",382   "sha256": "af8f7a0189ae069a11b0a93fdc8e06cff70911cc47896818c043d63c3b948449",383   "language": "Python",384   "lines": 33,385   "truncated": false,386   "block": 1,387   "row": 5936388  },389  {390   "path": "nnunetv2/dataset_conversion/datasets_for_integration_tests/Dataset999_IntegrationTest_Hippocampus.py",391   "sha256": "425ad3577d58a659260c9bbef555a8ae19a638b5905dedb1d6f8632a2ae654e5",392   "language": "Python",393   "lines": 27,394   "truncated": false,395   "block": 1,396   "row": 5759397  },398  {399   "path": "nnunetv2/dataset_conversion/generate_dataset_json.py",400   "sha256": "72e78a49b9a6f32f5ebc0a8312804ee49ecbd228b4e8b9537348b847dfe6fa15",401   "language": "Python",402   "lines": 111,403   "truncated": false,404   "block": 1,405   "row": 7297406  },407  {408   "path": "nnunetv2/ensembling/ensemble.py",409   "sha256": "8e7d4e6e41bea4a74c102a1de56aa634e52a6f8031c8b419f71866e989e818fc",410   "language": "Python",411   "lines": 207,412   "truncated": false,413   "block": 1,414   "row": 8498415  },416  {417   "path": "nnunetv2/evaluation/accumulate_cv_results.py",418   "sha256": "bafa26af2935673e1742aa50acf8371fd9e08240fc7ff6b366fcb57f160e5e78",419   "language": "Python",420   "lines": 58,421   "truncated": false,422   "block": 1,423   "row": 6879424  },425  {426   "path": "nnunetv2/evaluation/evaluate_predictions.py",427   "sha256": "bdce137cc297e33e126d648c625dd905a6c41d6aa80a521f4a629bbeca3df294",428   "language": "Python",429   "lines": 262,430   "truncated": false,431   "block": 1,432   "row": 8809433  },434  {435   "path": "nnunetv2/evaluation/find_best_configuration.py",436   "sha256": "59cf665c440e508df99221f94210684cf0cc4b7860c3f04bbb5978baa8913b87",437   "language": "Python",438   "lines": 339,439   "truncated": false,440   "block": 1,441   "row": 9279442  },443  {444   "path": "nnunetv2/experiment_planning/dataset_fingerprint/fingerprint_extractor.py",445   "sha256": "3c02d290f45c06b3d517f866ae4b9fc4e7fe39155ce8efc6ed1eafa8525e5900",446   "language": "Python",447   "lines": 211,448   "truncated": false,449   "block": 1,450   "row": 8771451  },452  {453   "path": "nnunetv2/experiment_planning/experiment_planners/default_experiment_planner.py",454   "sha256": "c37bb500e9ddd414beff4fae76992af847a8bfeef4b1dace3a052e5fba751554",455   "language": "Python",456   "lines": 603,457   "truncated": false,458   "block": 1,459   "row": 9670460  },461  {462   "path": "nnunetv2/experiment_planning/experiment_planners/network_topology.py",463   "sha256": "2140c9c6b20273bbf3052a72459954543d93790cc5269e0d8fbaddcfbd30aa8f",464   "language": "Python",465   "lines": 108,466   "truncated": false,467   "block": 1,468   "row": 7106469  },470  {471   "path": "nnunetv2/experiment_planning/experiment_planners/resampling/planners_no_resampling.py",472   "sha256": "f14c3cf05a40363acd8db6ff9c94cdfad22d78a94dc2bfd82a5ec2bfddcf3ae4",473   "language": "Python",474   "lines": 54,475   "truncated": false,476   "block": 1,477   "row": 6644478  },479  {480   "path": "nnunetv2/experiment_planning/experiment_planners/resampling/resample_with_torch.py",481   "sha256": "25d360daf2da56c79d535a9ac7eba5f0e8fd514dd8480e00fadf902846f814f3",482   "language": "Python",483   "lines": 181,484   "truncated": false,485   "block": 1,486   "row": 8308487  },488  {489   "path": "nnunetv2/experiment_planning/experiment_planners/resencUNet_planner.py",490   "sha256": "e9dec95ba75105a478319aae452d676b88d834721d38df4019bd8063d1f21aa9",491   "language": "Python",492   "lines": 26,493   "truncated": false,494   "block": 1,495   "row": 5798496  },497  {498   "path": "nnunetv2/experiment_planning/experiment_planners/residual_unets/residual_encoder_unet_planners.py",499   "sha256": "f2de43f8bc21a3bc8d7527380ff18015404a7a95561f7762a401cc87f740ddff",500   "language": "Python",501   "lines": 291,502   "truncated": false,503   "block": 1,504   "row": 9175505  },506  {507   "path": "nnunetv2/experiment_planning/like_nnssl.py",508   "sha256": "01e551bcb642e5b0eb70524dfe855100aa701b8fb8d5c50361ffc2f7b4de7737",509   "language": "Python",510   "lines": 512,511   "truncated": false,512   "block": 1,513   "row": 9471514  },515  {516   "path": "nnunetv2/experiment_planning/plan_and_preprocess_api.py",517   "sha256": "46fbca9631d6bec94ebd6e98906d0c6aac498497f4d9b2ee95057085f53dd914",518   "language": "Python",519   "lines": 171,520   "truncated": false,521   "block": 1,522   "row": 8526523  },524  {525   "path": "nnunetv2/experiment_planning/plan_and_preprocess_entrypoints.py",526   "sha256": "0e76f6f7e6d27bf5c1d4441ecc0a4e42cab5fd3bfa835c2cb2111de7214bf09e",527   "language": "Python",528   "lines": 235,529   "truncated": false,530   "block": 1,531   "row": 9270532  },533  {534   "path": "nnunetv2/experiment_planning/plans_for_pretraining/move_plans_between_datasets.py",535   "sha256": "6dec72fbd5e51a0f0de5e27b366f96b653ba634358d533899d37de68876473d7",536   "language": "Python",537   "lines": 82,538   "truncated": false,539   "block": 1,540   "row": 7266541  },542  {543   "path": "nnunetv2/experiment_planning/verify_dataset_integrity.py",544   "sha256": "1a6539853717e4cf90f2830893326b87a56bee61bbd6e84b275fd68019b425ad",545   "language": "Python",546   "lines": 239,547   "truncated": false,548   "block": 1,549   "row": 8824550  },551  {552   "path": "nnunetv2/imageio/base_reader_writer.py",553   "sha256": "ded57b2e4a14ab4775461f036449e6dda9062173736de3502f181a8364757198",554   "language": "Python",555   "lines": 107,556   "truncated": false,557   "block": 1,558   "row": 7612559  },560  {561   "path": "nnunetv2/imageio/natural_image_reader_writer.py",562   "sha256": "944cedccc7c471bced0aadcd861fab7bc84e9c08c571ab3e0da9947f204e4be3",563   "language": "Python",564   "lines": 81,565   "truncated": false,566   "block": 1,567   "row": 7066568  },569  {570   "path": "nnunetv2/imageio/nibabel_reader_writer.py",571   "sha256": "251b7edd0baff8c2b9790cafbafe361310636c2122bbe92be61426b2d6767500",572   "language": "Python",573   "lines": 222,574   "truncated": false,575   "block": 1,576   "row": 8452577  },578  {579   "path": "nnunetv2/imageio/reader_writer_registry.py",580   "sha256": "0190dbc7303a12d7c1afa5ba633d72bcaedabb4086fedacefffbe72b85b7e363",581   "language": "Python",582   "lines": 88,583   "truncated": false,584   "block": 1,585   "row": 7155586  },587  {588   "path": "nnunetv2/imageio/simpleitk_reader_writer.py",589   "sha256": "ef5afaf725119faa01256f385724c51d0b2ab2fd68551d669f49533229c1fab8",590   "language": "Python",591   "lines": 234,592   "truncated": false,593   "block": 1,594   "row": 8596595  },596  {597   "path": "nnunetv2/imageio/tif_reader_writer.py",598   "sha256": "b74e207550d209f851d3887557376ddd13f98a13bf3c681b03e792a786d0efd9",599   "language": "Python",600   "lines": 100,601   "truncated": false,602   "block": 1,603   "row": 7379604  },605  {606   "path": "nnunetv2/inference/JHU_inference.py",607   "sha256": "42ed5eeb1794459c1b0fd88393277b7820babab8ae48d09aff619079aca88f7b",608   "language": "Python",609   "lines": 197,610   "truncated": false,611   "block": 1,612   "row": 8285613  },614  {615   "path": "nnunetv2/inference/data_iterators.py",616   "sha256": "8437bd32ea1f055457d5e5d0b1e5b4fcbc51eeeb619586401bc9204e64cc501b",617   "language": "Python",618   "lines": 315,619   "truncated": false,620   "block": 1,621   "row": 9111622  },623  {624   "path": "nnunetv2/inference/examples.py",625   "sha256": "eb68c61ddc14b14006417b526a5a87363fcfe87a3a9cd8c4059c4e31f80a2419",626   "language": "Python",627   "lines": 100,628   "truncated": false,629   "block": 1,630   "row": 7832631  },632  {633   "path": "nnunetv2/inference/export_prediction.py",634   "sha256": "5b4db8e6f3e1a57f91babb21bca19cdc2c948d955c91fae24d0543a94f34fd7d",635   "language": "Python",636   "lines": 160,637   "truncated": false,638   "block": 1,639   "row": 8407640  },641  {642   "path": "nnunetv2/inference/predict_from_raw_data.py",643   "sha256": "c350e3202a7a67c3aef12e9206a744add442110ff8a4377c1f9640104b20a31f",644   "language": "Python",645   "lines": 1099,646   "truncated": false,647   "block": 1,648   "row": 9822649  },650  {651   "path": "nnunetv2/inference/sliding_window_prediction.py",652   "sha256": "df763e2077de4c616a546d5baa7707dff2abc678ec2c370d9bef4fa94cd00674",653   "language": "Python",654   "lines": 65,655   "truncated": false,656   "block": 1,657   "row": 6704658  },659  {660   "path": "nnunetv2/model_sharing/entry_points.py",661   "sha256": "f208bc7ed47b6a3dae45788a8153c8a08d1507977d7dcfed15200142c931aee0",662   "language": "Python",663   "lines": 61,664   "truncated": false,665   "block": 1,666   "row": 6977667  },668  {669   "path": "nnunetv2/model_sharing/model_download.py",670   "sha256": "1c69b2246957e85fabf1909a5d6b02651255ade64c7ae55b76af8bd9f8a1000b",671   "language": "Python",672   "lines": 39,673   "truncated": false,674   "block": 1,675   "row": 5980676  },677  {678   "path": "nnunetv2/model_sharing/model_export.py",679   "sha256": "9fbb7550a44f409bf97ab8375b0ef9268852e9cbcf4e8d1ae7d19ead4ee59a42",680   "language": "Python",681   "lines": 124,682   "truncated": false,683   "block": 1,684   "row": 7920685  },686  {687   "path": "nnunetv2/model_sharing/model_import.py",688   "sha256": "d5bea3c57923755557f58e86d73c4e2bc060fd15bb10d318ebab652ea83cc4aa",689   "language": "Python",690   "lines": 8,691   "truncated": false,692   "block": 1,693   "row": 5155694  },695  {696   "path": "nnunetv2/paths.py",697   "sha256": "9578aabd766402d21111ec04b3bb07a71b39ce618e5b06007fb04d86e3d18cd0",698   "language": "Python",699   "lines": 79,700   "truncated": false,701   "block": 1,702   "row": 6629703  },704  {705   "path": "nnunetv2/postprocessing/remove_connected_components.py",706   "sha256": "f8be44e499bc8b03df4f23eb68bce15a60d508829176267be337f57c3547e0a2",707   "language": "Python",708   "lines": 361,709   "truncated": false,710   "block": 1,711   "row": 9345712  },713  {714   "path": "nnunetv2/preprocessing/cropping/cropping.py",715   "sha256": "57298102d27dc19a88945399048dba6e07c73d35c0f4cad42c698995c4d2f1ac",716   "language": "Python",717   "lines": 39,718   "truncated": false,719   "block": 1,720   "row": 5817721  },722  {723   "path": "nnunetv2/preprocessing/normalization/default_normalization_schemes.py",724   "sha256": "e260a437360df5b64f2279c283c12b255abc75927d52546fc7fb90987a1745e5",725   "language": "Python",726   "lines": 104,727   "truncated": false,728   "block": 1,729   "row": 7358730  },731  {732   "path": "nnunetv2/preprocessing/normalization/map_channel_name_to_normalization.py",733   "sha256": "e195bc1f5cdfcf723b1a11c15e2539f15d11018bfcf20a758e18badca4b723fb",734   "language": "Python",735   "lines": 24,736   "truncated": false,737   "block": 1,738   "row": 5693739  },740  {741   "path": "nnunetv2/preprocessing/preprocessors/default_preprocessor.py",742   "sha256": "a2bb834d8a772ea47fab4281ddc83444d80d194ee84be53ee4ef6e689829695e",743   "language": "Python",744   "lines": 492,745   "truncated": false,746   "block": 1,747   "row": 9469748  },749  {750   "path": "nnunetv2/preprocessing/resampling/default_resampling.py",751   "sha256": "28f7214e82c6ab74eb565ab5662ae753886f067875fe96ea1ff07d7ccacd04e7",752   "language": "Python",753   "lines": 231,754   "truncated": false,755   "block": 1,756   "row": 8712757  },758  {759   "path": "nnunetv2/preprocessing/resampling/no_resampling.py",760   "sha256": "78838ffeefc3dfe065f0d667ec2613d26b7abf62344222fb44c98d7e6dfcb2e7",761   "language": "Python",762   "lines": 13,763   "truncated": false,764   "block": 1,765   "row": 5287766  },767  {768   "path": "nnunetv2/preprocessing/resampling/resample_torch.py",769   "sha256": "14da7db362c338fcd9276ff55358b46c8eb446a1153ab3a438ecc6e4eeafc9f8",770   "language": "Python",771   "lines": 174,772   "truncated": false,773   "block": 1,774   "row": 8104775  },776  {777   "path": "nnunetv2/preprocessing/resampling/utils.py",778   "sha256": "7f5cceddb94a028944f64074af41dc202d3ecba56e5c08dc7e2022e16ee1d141",779   "language": "Python",780   "lines": 15,781   "truncated": false,782   "block": 1,783   "row": 5530784  },785  {786   "path": "nnunetv2/preprocessing/sampling_locations/extract_sampling_locations.py",787   "sha256": "be837c1382768df158c3d20be5758aa76b58d56d1853ff472392c49730282fca",788   "language": "Python",789   "lines": 171,790   "truncated": false,791   "block": 1,792   "row": 8361793  },794  {795   "path": "nnunetv2/run/load_pretrained_weights.py",796   "sha256": "47012faae9240228240500ecffe46de9d0b8b0d6f3d384591664bf968e3ff8a1",797   "language": "Python",798   "lines": 73,799   "truncated": false,800   "block": 1,801   "row": 7024802  },803  {804   "path": "nnunetv2/run/run_training.py",805   "sha256": "29be2749495bc4aacb0223c1db4433295baa9d8981a4d13b60db8f7d3523d8d5",806   "language": "Python",807   "lines": 351,808   "truncated": false,809   "block": 1,810   "row": 9247811  },812  {813   "path": "nnunetv2/run/run_training_from_pretrained.py",814   "sha256": "8a5847c247b78aee9eaa0cc1858843ac279ab720a2a6bcb63fe96b4189d9d3cf",815   "language": "Python",816   "lines": 252,817   "truncated": false,818   "block": 1,819   "row": 8564820  },821  {822   "path": "nnunetv2/tests/integration_tests/add_lowres_and_cascade.py",823   "sha256": "5247c6d965b919e11398bf06d393043276b76535669402d266cd87b159df3042",824   "language": "Python",825   "lines": 42,826   "truncated": false,827   "block": 1,828   "row": 6338829  },830  {831   "path": "nnunetv2/tests/integration_tests/cleanup_integration_test.py",832   "sha256": "05294b36b4c9524209b1f8583db909fbe1bcd547bcd0419bb7d90f36d034b6e9",833   "language": "Python",834   "lines": 18,835   "truncated": false,836   "block": 1,837   "row": 5488838  },839  {840   "path": "nnunetv2/tests/integration_tests/lsf_commands.sh",841   "sha256": "9b23242ed31e56c2b50b589be48c08008f2292f5863f8e78802d6bb637e16d37",842   "language": "Shell",843   "lines": 10,844   "truncated": false,845   "block": 1,846   "row": 11670847  },848  {849   "path": "nnunetv2/tests/integration_tests/prepare_integration_tests.sh",850   "sha256": "9ee91888287f3c1caa662c9c2332dcc8e80d4b0d984e4981ce445dae4b56b5c4",851   "language": "Shell",852   "lines": 18,853   "truncated": false,854   "block": 1,855   "row": 11502856  },857  {858   "path": "nnunetv2/tests/integration_tests/run_integration_test.sh",859   "sha256": "778b9fb65049c20745921996bd11195ed58b2f26d67d95aff32413d1f7b88453",860   "language": "Shell",861   "lines": 27,862   "truncated": false,863   "block": 1,864   "row": 11630865  },866  {867   "path": "nnunetv2/tests/integration_tests/run_integration_test_bestconfig_inference.py",868   "sha256": "acfbfba79a943003d1d40b0c140f2790b17948dcac2f4cb322a43f253d93609e",869   "language": "Python",870   "lines": 75,871   "truncated": false,872   "block": 1,873   "row": 7223874  },875  {876   "path": "nnunetv2/tests/integration_tests/run_integration_test_trainingOnly_DDP.sh",877   "sha256": "99494db232e67bf1ef81046125863228612151df87c3221cad0372679e294f2a",878   "language": "Shell",879   "lines": 1,880   "truncated": false,881   "block": 1,882   "row": 11108883  },884  {885   "path": "nnunetv2/tests/integration_tests/run_nnunet_inference.py",886   "sha256": "9f1eb418c303e55113653273f2ffbb76f3caae0bfa837186f1475e33f2599848",887   "language": "Python",888   "lines": 46,889   "truncated": false,890   "block": 1,891   "row": 6154892  },893  {894   "path": "nnunetv2/tests/test_copy_file_if_newer.py",895   "sha256": "c540f7e0b7d7684910596a749c85c5395be45eca2c7943ed4346d6b948f745ad",896   "language": "Python",897   "lines": 53,898   "truncated": false,899   "block": 1,900   "row": 6404901  },902  {903   "path": "nnunetv2/tests/test_find_objects.py",904   "sha256": "c77d1e98f183ce4a77d56217735e01c0f2f78123d4e42c05e7bc076ddbc54601",905   "language": "Python",906   "lines": 140,907   "truncated": false,908   "block": 1,909   "row": 7450910  },911  {912   "path": "nnunetv2/tests/test_foreground_locations.py",913   "sha256": "2fbb147c4e30e8265c4ee57704ac962202574bfc9eb96968e444e935b8dbb1f3",914   "language": "Python",915   "lines": 521,916   "truncated": false,917   "block": 1,918   "row": 9518919  },920  {921   "path": "nnunetv2/tests/test_natural_image_tiff_compression.py",922   "sha256": "db32cb05814482a6b8747f1f1c5c0a038b349bc7fef8910a8ca5bc331b7c608c",923   "language": "Python",924   "lines": 148,925   "truncated": false,926   "block": 1,927   "row": 7770928  },929  {930   "path": "nnunetv2/tests/test_paths.py",931   "sha256": "14c55695ec3c102e0f1e87688d97583cbc90067b5a5bf1ce2704d08f3d0648e1",932   "language": "Python",933   "lines": 45,934   "truncated": false,935   "block": 1,936   "row": 6251937  },938  {939   "path": "nnunetv2/tests/test_resampling.py",940   "sha256": "4c0f6a847d5709f5b306000e017725d384ea66b3034b96da4f2da3000711d414",941   "language": "Python",942   "lines": 273,943   "truncated": false,944   "block": 1,945   "row": 9039946  },947  {948   "path": "nnunetv2/training/data_augmentation/compute_initial_patch_size.py",949   "sha256": "4da8a4fbb4db5bd5a428a596793c0bd685d360ec8b24bd4be7495fda59352e9f",950   "language": "Python",951   "lines": 24,952   "truncated": false,953   "block": 1,954   "row": 5807955  },956  {957   "path": "nnunetv2/training/data_augmentation/custom_transforms/cascade_transforms.py",958   "sha256": "246f051c507492f6861ae505535b13fa1e2172f13e4407364212df2c8d8ae2e7",959   "language": "Python",960   "lines": 136,961   "truncated": false,962   "block": 1,963   "row": 8024964  },965  {966   "path": "nnunetv2/training/data_augmentation/custom_transforms/deep_supervision_donwsampling.py",967   "sha256": "f2f85b8a092e4fee07b1c6763dd44566592a1a780a74cec20f7e877fb1d4ba9b",968   "language": "Python",969   "lines": 55,970   "truncated": false,971   "block": 1,972   "row": 6577973  },974  {975   "path": "nnunetv2/training/data_augmentation/custom_transforms/masking.py",976   "sha256": "e0a648d7875ae44c17ffb9af200ab0e1dab263c4f29678075db7a6819a243031",977   "language": "Python",978   "lines": 22,979   "truncated": false,980   "block": 1,981   "row": 5650982  },983  {984   "path": "nnunetv2/training/data_augmentation/custom_transforms/region_based_training.py",985   "sha256": "7b0802c0791b8a7e253e1ad1e9ee2cad6c95e8882e56b0b9e556d0d2220db4e6",986   "language": "Python",987   "lines": 31,988   "truncated": false,989   "block": 1,990   "row": 5918991  },992  {993   "path": "nnunetv2/training/data_augmentation/custom_transforms/transforms_for_dummy_2d.py",994   "sha256": "63443f7e76981ee4eed59649ab8b6cef09bddd63da8d9ccace5d836afb82532f",995   "language": "Python",996   "lines": 45,997   "truncated": false,998   "block": 1,999   "row": 64961000  },1001  {1002   "path": "nnunetv2/training/dataloading/data_loader.py",1003   "sha256": "6f35e60da43c9c7c3aa2fd71c52e451ac898265b6c9b1ccf72f9b90d3b0506e4",1004   "language": "Python",1005   "lines": 217,1006   "truncated": false,1007   "block": 1,1008   "row": 87531009  },1010  {1011   "path": "nnunetv2/training/dataloading/foreground_locations.py",1012   "sha256": "17e6f1d2698d432e3b380d204e1c3a76858e906ca0edcde5be64cf43bca25258",1013   "language": "Python",1014   "lines": 586,1015   "truncated": false,1016   "block": 1,1017   "row": 95641018  },1019  {1020   "path": "nnunetv2/training/dataloading/nnunet_dataset.py",1021   "sha256": "8f9e6123ae83e33ea3a3fc48b8285a6e80eb52b9e90ead19148806d5613d20aa",1022   "language": "Python",1023   "lines": 530,1024   "truncated": false,1025   "block": 1,1026   "row": 93141027  },1028  {1029   "path": "nnunetv2/training/dataloading/utils.py",1030   "sha256": "d6d2518e0092c85605ba6ae5b98f3a11d74d46015988e350ffa6614f56ae42e1",1031   "language": "Python",1032   "lines": 71,1033   "truncated": false,1034   "block": 1,1035   "row": 67541036  },1037  {1038   "path": "nnunetv2/training/logging/nnunet_logger.py",1039   "sha256": "128e720e7fd23b57ffe0279f7b1e45ccaeff5c11aee8d42dfb2ba69750460174",1040   "language": "Python",1041   "lines": 303,1042   "truncated": false,1043   "block": 1,1044   "row": 86921045  },1046  {1047   "path": "nnunetv2/training/loss/compound_losses.py",1048   "sha256": "f7d4516748b62c29bbf281c19ae1ba1f109219820c00ee4fc88ceee651ccb092",1049   "language": "Python",1050   "lines": 156,1051   "truncated": false,1052   "block": 1,1053   "row": 77621054  },1055  {1056   "path": "nnunetv2/training/loss/deep_supervision.py",1057   "sha256": "41fd5993faaf3e482ed370bd2af97b6cb943bb59a92cc48f7712802283325a9d",1058   "language": "Python",1059   "lines": 29,1060   "truncated": false,1061   "block": 1,1062   "row": 59451063  },1064  {1065   "path": "nnunetv2/training/loss/dice.py",1066   "sha256": "cbf124bcfb093516b8066942959a45a1e3bfbcee5b96cc5de369330ee31cdbd2",1067   "language": "Python",1068   "lines": 200,1069   "truncated": false,1070   "block": 1,1071   "row": 79991072  },1073  {1074   "path": "nnunetv2/training/loss/robust_ce_loss.py",1075   "sha256": "d0f74c94846f03d19658c01c429260ca18c0d7bd2fcc59dab61c82d8d588acaa",1076   "language": "Python",1077   "lines": 32,1078   "truncated": false,1079   "block": 1,1080   "row": 58051081  },1082  {1083   "path": "nnunetv2/training/lr_scheduler/polylr.py",1084   "sha256": "29beff3ce0b8b2881012092752255bae0c276a6fb68da9c72643a8e3054ddcf3",1085   "language": "Python",1086   "lines": 26,1087   "truncated": false,1088   "block": 1,1089   "row": 56731090  },1091  {1092   "path": "nnunetv2/training/lr_scheduler/warmup.py",1093   "sha256": "c00817feabd64e46cc22352395f5cb3e6d8db0e4f02887a64369e7864fc17b85",1094   "language": "Python",1095   "lines": 143,1096   "truncated": false,1097   "block": 1,1098   "row": 75661099  },1100  {1101   "path": "nnunetv2/training/nnUNetTrainer/nnUNetTrainer.py",1102   "sha256": "cf93784ed047f38fe17dff33d532337a991e046e082602d5f9c86e2827e4213b",1103   "language": "Python",1104   "lines": 1505,1105   "truncated": false,1106   "block": 1,1107   "row": 98431108  },1109  {1110   "path": "nnunetv2/training/nnUNetTrainer/pretraining/dynamicPretrainedTrainer.py",1111   "sha256": "0aed6248fece3909d1a80728e7b6fea28c67c054d086a2b3036db451f1cbfb53",1112   "language": "Python",1113   "lines": 455,1114   "truncated": false,1115   "block": 1,1116   "row": 94151117  },1118  {1119   "path": "nnunetv2/training/nnUNetTrainer/pretraining/pretrainedTrainer.py",1120   "sha256": "7aca6881b25469b48726c12676fc1059e9c1f3dd5576d31024af13711a0ffa66",1121   "language": "Python",1122   "lines": 760,1123   "truncated": false,1124   "block": 1,1125   "row": 96961126  },1127  {1128   "path": "nnunetv2/training/nnUNetTrainer/pretraining/thrp_primusx_finetuning.py",1129   "sha256": "73939d29546cbc429c06c6e635aa1d98f4e876076096afd64337f7ab5da1020a",1130   "language": "Python",1131   "lines": 287,1132   "truncated": false,1133   "block": 1,1134   "row": 89061135  },1136  {1137   "path": "nnunetv2/training/nnUNetTrainer/primus/primus_trainers.py",1138   "sha256": "b4f7466823002ba6d90c1cd968f6a5c34dc780bdcb0a0c8978f939886de378a0",1139   "language": "Python",1140   "lines": 511,1141   "truncated": false,1142   "block": 1,1143   "row": 91841144  },1145  {1146   "path": "nnunetv2/training/nnUNetTrainer/variants/benchmarking/nnUNetTrainerBenchmark_5epochs.py",1147   "sha256": "41c61c88d8a7db1f3fa175b2287d5682f3d22162556b523844884c757f420154",1148   "language": "Python",1149   "lines": 67,1150   "truncated": false,1151   "block": 1,1152   "row": 67551153  },1154  {1155   "path": "nnunetv2/training/nnUNetTrainer/variants/benchmarking/nnUNetTrainerBenchmark_5epochs_noDataLoading.py",1156   "sha256": "902e6f8731ccb7f420924e6ec6011d953c99ba608ab81f628bca7f3a318c800f",1157   "language": "Python",1158   "lines": 68,1159   "truncated": false,1160   "block": 1,1161   "row": 66221162  },1163  {1164   "path": "nnunetv2/training/nnUNetTrainer/variants/competitions/aortaseg24.py",1165   "sha256": "8f5cbb5d73b1a4c0e1975f29518f205e4850a95639fd295a0ada5d04428a88e1",1166   "language": "Python",1167   "lines": 5,1168   "truncated": false,1169   "block": 1,1170   "row": 52321171  },1172  {1173   "path": "nnunetv2/training/nnUNetTrainer/variants/data_augmentation/nnUNetTrainerDA5.py",1174   "sha256": "a9b9a452a94ed43b959715add5f1b05533d694dd82e8504f00532979b9c1022e",1175   "language": "Python",1176   "lines": 390,1177   "truncated": false,1178   "block": 1,1179   "row": 92021180  },1181  {1182   "path": "nnunetv2/training/nnUNetTrainer/variants/data_augmentation/nnUNetTrainerDAOrd0.py",1183   "sha256": "443741aed64034afb9f24b3922a4a9de8912908580bc31218915b2c3ffa88bd4",1184   "language": "Python",1185   "lines": 191,1186   "truncated": false,1187   "block": 1,1188   "row": 82131189  },1190  {1191   "path": "nnunetv2/training/nnUNetTrainer/variants/data_augmentation/nnUNetTrainerNoDA.py",1192   "sha256": "c7153eba175fe9869de549e9a425d050a05a1b23fd96ec0bbdf792398ff62129",1193   "language": "Python",1194   "lines": 34,1195   "truncated": false,1196   "block": 1,1197   "row": 60881198  },1199  {1200   "path": "nnunetv2/training/nnUNetTrainer/variants/data_augmentation/nnUNetTrainerNoMirroring.py",

Showing the first 1,200 of 1524 lines. Download the file for the rest.