Team Ai
Datasetpublic

OpenScientificCodeRegistry/Database

Open Scientific Code Registry (OSCR): the authors' scripts The code published by the authors of open-access neuroscience papers, as found and verified by Open Scientific Code Registry (OSCR). Each file is here exactly as it is at the source, at the verified commit, under the license of its repository. 421,275 unique files (3,782 MB of text) from 8,849 repositories, in 24 Parquet block(s). Only files whose repository's license allows redistribution, confirmed by the repository's… See the full description on the dataset page: https://huggingface.co/datasets/OpenScientificCodeRegistry/Database.

sourceHugging Faceotherupdated 2d agoView on Hugging Face
0likes5.6kdownloads
github.com__mafortin__gouhfi.json1290 linesDownload Raw Back to a2
1{2 "format": "oscr-script-manifest/1",3 "repository": "github.com/mafortin/gouhfi",4 "url": "https://github.com/mafortin/GOUHFI",5 "host": "github.com",6 "commit": "1eb71b642bcd3b6c92dbf65e4b69c8cf52847205",7 "license": "Apache-2.0",8 "license_confirmed_by": "license file LICENSE",9 "redistribution": "yes",10 "files": [11  {12   "path": "LICENSE",13   "sha256": "c71d239df91726fc519c6eb72d318ec65820627232b2f796219e87dcf35d0ab4",14   "language": "License",15   "lines": 201,16   "truncated": false,17   "block": 1,18   "row": 221619  },20  {21   "path": "README.md",22   "sha256": "040db67701a1179a2ad590b44b1ea4444c38edbe6584bad11867370296fe1678",23   "language": "Text",24   "lines": 216,25   "truncated": false,26   "block": 18,27   "row": 1117928  },29  {30   "path": "data_utils/add_extra_cerebral_label.py",31   "sha256": "e91c9b8a18cf2f9f1e7dc4261b5c31f6e8d5489d143f011e2efd3679052ddd94",32   "language": "Python",33   "lines": 166,34   "truncated": false,35   "block": 17,36   "row": 3182437  },38  {39   "path": "data_utils/brain_extraction_antspynet.py",40   "sha256": "1b4e8fbc4fafc63f05c7629290ca78608f1f0e13a7b62cce98999ed2a7b5610c",41   "language": "Python",42   "lines": 122,43   "truncated": false,44   "block": 17,45   "row": 2941946  },47  {48   "path": "data_utils/conform_images.py",49   "sha256": "731980d2a49cbcc93d615e69b7f9fedec07d9eb00a70e1bd5d6935102d3616ee",50   "language": "Python",51   "lines": 104,52   "truncated": false,53   "block": 17,54   "row": 2736655  },56  {57   "path": "data_utils/conform_labels.py",58   "sha256": "62b560145f4dc1c765b25219c8412373b7e270162e486b59bb3cf16b78f6fc82",59   "language": "Python",60   "lines": 68,61   "truncated": false,62   "block": 17,63   "row": 2512364  },65  {66   "path": "data_utils/get_volume_values.py",67   "sha256": "bf56aa4acb5f2f91069c0fe995d67fef49aa2a271c15a07c410ddbd1dd9330d4",68   "language": "Python",69   "lines": 159,70   "truncated": false,71   "block": 17,72   "row": 2912373  },74  {75   "path": "data_utils/preprocessing_pipeline.py",76   "sha256": "61b9dfb87923e7f6cf691fd602ebb361619ced5c383929388ebc693d105e5305",77   "language": "Python",78   "lines": 80,79   "truncated": false,80   "block": 17,81   "row": 2637982  },83  {84   "path": "data_utils/remove_keep_reindex_labels.py",85   "sha256": "47e1c4735c36e811766e70aa0e27c3c503f8104f256938c4a59f937588e66866",86   "language": "Python",87   "lines": 112,88   "truncated": false,89   "block": 17,90   "row": 2731891  },92  {93   "path": "data_utils/rename_files_nnunet_convention.py",94   "sha256": "07323f14f5c4bc45b1b425fde0f6bf7a90e9641ca7e7090d25814074fb22aa7d",95   "language": "Python",96   "lines": 69,97   "truncated": false,98   "block": 17,99   "row": 24325100  },101  {102   "path": "data_utils/reorder_labels_freesurfer_lut.py",103   "sha256": "c5644a4e50642157ce7502ddd5be7d785a0d3bf49bc80fb3e90ba1ae1cb942fe",104   "language": "Python",105   "lines": 125,106   "truncated": false,107   "block": 17,108   "row": 28689109  },110  {111   "path": "docker/entrypoint.sh",112   "sha256": "443216bc14b084e5bb393fa5b8fb900a13972e67b0f16dd06165480303ec193a",113   "language": "Shell",114   "lines": 14,115   "truncated": false,116   "block": 18,117   "row": 8987118  },119  {120   "path": "nnunetv2/batch_running/benchmarking/generate_benchmarking_commands.py",121   "sha256": "14abb1eb4e966e9ac9789003ad6b70548978061d10017e609f91a0cf0eb88974",122   "language": "Python",123   "lines": 41,124   "truncated": false,125   "block": 3,126   "row": 20223127  },128  {129   "path": "nnunetv2/batch_running/benchmarking/summarize_benchmark_results.py",130   "sha256": "241809f5cc0ef6d16c3c6cc16ce2b69a51c969551cb4b8a89d5b4445589ebb05",131   "language": "Python",132   "lines": 70,133   "truncated": false,134   "block": 3,135   "row": 21530136  },137  {138   "path": "nnunetv2/batch_running/collect_results_custom_Decathlon.py",139   "sha256": "ae92bb5d1333cd266ac4bc4e539b905d42d1fe2eb85d533501bc171247813b4c",140   "language": "Python",141   "lines": 112,142   "truncated": false,143   "block": 12,144   "row": 14500145  },146  {147   "path": "nnunetv2/batch_running/collect_results_custom_Decathlon_2d.py",148   "sha256": "d4bf22f3ffec8578bd0051c04b5b04d2e35997c041d601a1e8ce4936a3060f85",149   "language": "Python",150   "lines": 18,151   "truncated": false,152   "block": 3,153   "row": 18623154  },155  {156   "path": "nnunetv2/batch_running/generate_lsf_runs_customDecathlon.py",157   "sha256": "447a11baa95717382fd08e67a333611b60820ebbd2a8a397592e68636413cc78",158   "language": "Python",159   "lines": 84,160   "truncated": false,161   "block": 17,162   "row": 25472163  },164  {165   "path": "nnunetv2/batch_running/release_trainings/nnunetv2_v1/collect_results.py",166   "sha256": "0b04206863b2e762e80011c6b1d8557cfc0e4cfd5de7c63c309b602ca49edbb0",167   "language": "Python",168   "lines": 113,169   "truncated": false,170   "block": 3,171   "row": 23383172  },173  {174   "path": "nnunetv2/batch_running/release_trainings/nnunetv2_v1/generate_lsf_commands.py",175   "sha256": "02e2c82613e4aa810295e8b0940605231b7ff6c7b8e34fb2bf1245882f6225eb",176   "language": "Python",177   "lines": 93,178   "truncated": false,179   "block": 3,180   "row": 22026181  },182  {183   "path": "nnunetv2/configuration.py",184   "sha256": "c62f73b1bc1111b0bc9c3dfe5c8d1a481047bbb2c128b6017ede97da2af17beb",185   "language": "Python",186   "lines": 10,187   "truncated": false,188   "block": 1,189   "row": 5326190  },191  {192   "path": "nnunetv2/dataset_conversion/Dataset027_ACDC.py",193   "sha256": "833c9bbbb0fe3355e550368a8af1d0340058852e91de44f13d9e72b5886436b0",194   "language": "Python",195   "lines": 114,196   "truncated": false,197   "block": 1,198   "row": 7309199  },200  {201   "path": "nnunetv2/dataset_conversion/Dataset073_Fluo_C3DH_A549_SIM.py",202   "sha256": "83417929feb87ef483488a4023bac343f097f60bf76b3a625eae7402cac39c91",203   "language": "Python",204   "lines": 85,205   "truncated": false,206   "block": 3,207   "row": 22334208  },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/Dataset120_RoadSegmentation.py",229   "sha256": "a369cdbe6cdcb95c35064b85c446c1cd5ddc7e6891b096548d2cb5525fc35d07",230   "language": "Python",231   "lines": 87,232   "truncated": false,233   "block": 3,234   "row": 21685235  },236  {237   "path": "nnunetv2/dataset_conversion/Dataset137_BraTS21.py",238   "sha256": "cd07a21164e4585d974afb5642c60a0aa33adeda3a95d120aa66e800c440db73",239   "language": "Python",240   "lines": 98,241   "truncated": false,242   "block": 3,243   "row": 22162244  },245  {246   "path": "nnunetv2/dataset_conversion/Dataset218_Amos2022_task1.py",247   "sha256": "105f57f47808a67c577d03a3d2a1be5a0fd85f36d6765ed9673568bc49769dcf",248   "language": "Python",249   "lines": 70,250   "truncated": false,251   "block": 3,252   "row": 21937253  },254  {255   "path": "nnunetv2/dataset_conversion/Dataset219_Amos2022_task2.py",256   "sha256": "1074b6242df81dd63ca207f088e0a3752e22eeb25a52abf6ae09f808b67e8e5a",257   "language": "Python",258   "lines": 65,259   "truncated": false,260   "block": 3,261   "row": 21782262  },263  {264   "path": "nnunetv2/dataset_conversion/Dataset220_KiTS2023.py",265   "sha256": "9eb2d979548987343da75f46ff60d4150be83875142db24d88dd64086ecce06c",266   "language": "Python",267   "lines": 50,268   "truncated": false,269   "block": 3,270   "row": 20279271  },272  {273   "path": "nnunetv2/dataset_conversion/Dataset221_AutoPETII_2023.py",274   "sha256": "adb24656233a4ac01c0a7398076c2c8df43082b69e1facb1c1cce923476affe5",275   "language": "Python",276   "lines": 70,277   "truncated": false,278   "block": 1,279   "row": 6838280  },281  {282   "path": "nnunetv2/dataset_conversion/Dataset223_AMOS2022postChallenge.py",283   "sha256": "6c1b541a62b5be4b948e0f4874245610e6a5b76659df60558890efb339c10d1c",284   "language": "Python",285   "lines": 59,286   "truncated": false,287   "block": 1,288   "row": 6606289  },290  {291   "path": "nnunetv2/dataset_conversion/Dataset988_dummyDataset4.py",292   "sha256": "b6a2fbe51d9007d0917cac4ce6da87dd0850798052a94798d8c82335c8befe11",293   "language": "Python",294   "lines": 32,295   "truncated": false,296   "block": 1,297   "row": 5937298  },299  {300   "path": "nnunetv2/dataset_conversion/convert_MSD_dataset.py",301   "sha256": "449bbedc74fb184010f546ba8587bce7d4e89757e22a00021e16c78af1d37d2f",302   "language": "Python",303   "lines": 132,304   "truncated": false,305   "block": 3,306   "row": 23602307  },308  {309   "path": "nnunetv2/dataset_conversion/convert_raw_dataset_from_old_nnunet_format.py",310   "sha256": "a007dc0cf6d3e383e9fbc0ad300e7a0b45ce95711ac969ec06f847699bb1cda6",311   "language": "Python",312   "lines": 53,313   "truncated": false,314   "block": 1,315   "row": 6722316  },317  {318   "path": "nnunetv2/dataset_conversion/datasets_for_integration_tests/Dataset996_IntegrationTest_Hippocampus_regions_ignore.py",319   "sha256": "bbd4605b24d97ba49afeac37647178330bbed52450bcc502fa269326b8c9e7ea",320   "language": "Python",321   "lines": 75,322   "truncated": false,323   "block": 3,324   "row": 21508325  },326  {327   "path": "nnunetv2/dataset_conversion/datasets_for_integration_tests/Dataset997_IntegrationTest_Hippocampus_regions.py",328   "sha256": "0fdc2e99d835b33d8db1f8992a13d60619a587cd2f1b3230f1fea2d0e478f0da",329   "language": "Python",330   "lines": 37,331   "truncated": false,332   "block": 1,333   "row": 5988334  },335  {336   "path": "nnunetv2/dataset_conversion/datasets_for_integration_tests/Dataset998_IntegrationTest_Hippocampus_ignore.py",337   "sha256": "af8f7a0189ae069a11b0a93fdc8e06cff70911cc47896818c043d63c3b948449",338   "language": "Python",339   "lines": 33,340   "truncated": false,341   "block": 1,342   "row": 5936343  },344  {345   "path": "nnunetv2/dataset_conversion/datasets_for_integration_tests/Dataset999_IntegrationTest_Hippocampus.py",346   "sha256": "425ad3577d58a659260c9bbef555a8ae19a638b5905dedb1d6f8632a2ae654e5",347   "language": "Python",348   "lines": 27,349   "truncated": false,350   "block": 1,351   "row": 5759352  },353  {354   "path": "nnunetv2/dataset_conversion/generate_dataset_json.py",355   "sha256": "a24fda3e897fd6e010da1758c3a10bbd70ae57e1a1f9bb08a8e9b1ebae1dd1e7",356   "language": "Python",357   "lines": 103,358   "truncated": false,359   "block": 3,360   "row": 22206361  },362  {363   "path": "nnunetv2/ensembling/ensemble.py",364   "sha256": "2a6ea82587a7c39ffb4c29d4a6765931871a4b9bc72d2d364bb1e83580251317",365   "language": "Python",366   "lines": 206,367   "truncated": false,368   "block": 3,369   "row": 25345370  },371  {372   "path": "nnunetv2/evaluation/accumulate_cv_results.py",373   "sha256": "bafa26af2935673e1742aa50acf8371fd9e08240fc7ff6b366fcb57f160e5e78",374   "language": "Python",375   "lines": 58,376   "truncated": false,377   "block": 1,378   "row": 6879379  },380  {381   "path": "nnunetv2/evaluation/evaluate_predictions.py",382   "sha256": "61d928b49368ef5b820cef97b3acf332bb71f331f7699cd73f574ee4154bf956",383   "language": "Python",384   "lines": 264,385   "truncated": false,386   "block": 18,387   "row": 1261388  },389  {390   "path": "nnunetv2/evaluation/find_best_configuration.py",391   "sha256": "735bb40b00a69838af26fcbd642a915051edbad6eb9334bd9a2e1911a92190c4",392   "language": "Python",393   "lines": 333,394   "truncated": false,395   "block": 3,396   "row": 26932397  },398  {399   "path": "nnunetv2/experiment_planning/dataset_fingerprint/fingerprint_extractor.py",400   "sha256": "225e6a3634ee63e6356df13a0ad795559b7588f889693e835df6522cc9d9e332",401   "language": "Python",402   "lines": 210,403   "truncated": false,404   "block": 12,405   "row": 18645406  },407  {408   "path": "nnunetv2/experiment_planning/experiment_planners/default_experiment_planner.py",409   "sha256": "d679b91be97c4a83ab2a32eb45fddb7c20ac95444d29fc09efec8699e23fd83f",410   "language": "Python",411   "lines": 593,412   "truncated": false,413   "block": 3,414   "row": 27697415  },416  {417   "path": "nnunetv2/experiment_planning/experiment_planners/network_topology.py",418   "sha256": "2140c9c6b20273bbf3052a72459954543d93790cc5269e0d8fbaddcfbd30aa8f",419   "language": "Python",420   "lines": 108,421   "truncated": false,422   "block": 1,423   "row": 7106424  },425  {426   "path": "nnunetv2/experiment_planning/experiment_planners/resencUNet_planner.py",427   "sha256": "4937ef22d6286d99d1190515387d0ba695c945467d0ae2b4d2f2bb8d79ac4c38",428   "language": "Python",429   "lines": 235,430   "truncated": false,431   "block": 3,432   "row": 26360433  },434  {435   "path": "nnunetv2/experiment_planning/experiment_planners/residual_unets/residual_encoder_unet_planners.py",436   "sha256": "07a2769aef2a144105826c8f95cdb0898369fde5411ff900e0912bc936ebb2b2",437   "language": "Python",438   "lines": 313,439   "truncated": false,440   "block": 18,441   "row": 3017442  },443  {444   "path": "nnunetv2/experiment_planning/plan_and_preprocess_api.py",445   "sha256": "9c8720fdd4819c044635c7bf23677c925ad551767fb5d2218aa481afef812195",446   "language": "Python",447   "lines": 150,448   "truncated": false,449   "block": 3,450   "row": 24792451  },452  {453   "path": "nnunetv2/experiment_planning/plan_and_preprocess_entrypoints.py",454   "sha256": "211a32258a928c48bf4fab5b84523d30b7f777caf51a2df83c17d2f4b69a3bcc",455   "language": "Python",456   "lines": 204,457   "truncated": false,458   "block": 18,459   "row": 2639460  },461  {462   "path": "nnunetv2/experiment_planning/plans_for_pretraining/move_plans_between_datasets.py",463   "sha256": "4c9294249445ab054e0670d2f28856a7158b47b53873db088382ccd70fef9191",464   "language": "Python",465   "lines": 83,466   "truncated": false,467   "block": 3,468   "row": 22564469  },470  {471   "path": "nnunetv2/experiment_planning/verify_dataset_integrity.py",472   "sha256": "0b1ecab87b7123e1d3a17674348d03e79a101dfbaf3aef41d4f54be54e089fac",473   "language": "Python",474   "lines": 234,475   "truncated": false,476   "block": 18,477   "row": 1117478  },479  {480   "path": "nnunetv2/imageio/base_reader_writer.py",481   "sha256": "83da631300b449df48c0bd940d362c3735d7c756d01c5c3f2d081bb0fc64f64c",482   "language": "Python",483   "lines": 107,484   "truncated": false,485   "block": 3,486   "row": 23356487  },488  {489   "path": "nnunetv2/imageio/natural_image_reader_writer.py",490   "sha256": "6074df4922384d041fb67730e6a388cfade577d1b04c2ad7dc6d6c40047e1cb7",491   "language": "Python",492   "lines": 73,493   "truncated": false,494   "block": 3,495   "row": 21604496  },497  {498   "path": "nnunetv2/imageio/nibabel_reader_writer.py",499   "sha256": "9c1a321e1a34d5303e322c38ca701ef36a4c3a950ab525d7cbc348fb578d14d7",500   "language": "Python",501   "lines": 204,502   "truncated": false,503   "block": 17,504   "row": 31948505  },506  {507   "path": "nnunetv2/imageio/reader_writer_registry.py",508   "sha256": "3b21e1aa5d20d73a92691f4ef111fca3dc5b0d95bc8f651ee91d6254ffdeb682",509   "language": "Python",510   "lines": 79,511   "truncated": false,512   "block": 3,513   "row": 22048514  },515  {516   "path": "nnunetv2/imageio/simpleitk_reader_writer.py",517   "sha256": "86d7984540ca767523dfca1d6a4def9bd42f290030017bec01a95e9f3945a65f",518   "language": "Python",519   "lines": 129,520   "truncated": false,521   "block": 17,522   "row": 29174523  },524  {525   "path": "nnunetv2/imageio/tif_reader_writer.py",526   "sha256": "0e689cf26ba8e59cdccb351c073cac57a7377a8b74dd75684ff9f15ea392b06a",527   "language": "Python",528   "lines": 100,529   "truncated": false,530   "block": 3,531   "row": 22738532  },533  {534   "path": "nnunetv2/inference/data_iterators.py",535   "sha256": "50d4855403817f35705fa5706de227cca3f6224e4d67a7b2f0836397c07ba787",536   "language": "Python",537   "lines": 313,538   "truncated": false,539   "block": 18,540   "row": 2523541  },542  {543   "path": "nnunetv2/inference/examples.py",544   "sha256": "ad30b3850344e96d6ee2d7d6a0b7e1d4dceafad777e8555672038bacf6ef051a",545   "language": "Python",546   "lines": 102,547   "truncated": false,548   "block": 6,549   "row": 44151550  },551  {552   "path": "nnunetv2/inference/export_prediction.py",553   "sha256": "a7c9e062e757ee3446942f593cbb7ab3b8c1f207dfaee819735952ec22020f66",554   "language": "Python",555   "lines": 145,556   "truncated": false,557   "block": 3,558   "row": 24662559  },560  {561   "path": "nnunetv2/inference/predict_from_raw_data.py",562   "sha256": "e57d9825014fb2ddddee5d4ce284568a3ab8f89a1a9597f12cfade7358087647",563   "language": "Python",564   "lines": 954,565   "truncated": false,566   "block": 18,567   "row": 5467568  },569  {570   "path": "nnunetv2/inference/sliding_window_prediction.py",571   "sha256": "c36fa09cc4b8f21d337edd934b5e1931072ed81ec07766af79cfd2d7db343eb3",572   "language": "Python",573   "lines": 65,574   "truncated": false,575   "block": 3,576   "row": 21128577  },578  {579   "path": "nnunetv2/model_sharing/entry_points.py",580   "sha256": "f208bc7ed47b6a3dae45788a8153c8a08d1507977d7dcfed15200142c931aee0",581   "language": "Python",582   "lines": 61,583   "truncated": false,584   "block": 1,585   "row": 6977586  },587  {588   "path": "nnunetv2/model_sharing/model_download.py",589   "sha256": "13cab02343cc3c7a1cdac547b70fe7d9d12416c891f6d9e22a7d6c7a37a78c9a",590   "language": "Python",591   "lines": 47,592   "truncated": false,593   "block": 3,594   "row": 19993595  },596  {597   "path": "nnunetv2/model_sharing/model_export.py",598   "sha256": "9fbb7550a44f409bf97ab8375b0ef9268852e9cbcf4e8d1ae7d19ead4ee59a42",599   "language": "Python",600   "lines": 124,601   "truncated": false,602   "block": 1,603   "row": 7920604  },605  {606   "path": "nnunetv2/model_sharing/model_import.py",607   "sha256": "47856f523e0acdcc7935142d94d22ce4bcc8463d6c61f0299f588b1132f2d1fa",608   "language": "Python",609   "lines": 8,610   "truncated": false,611   "block": 3,612   "row": 17696613  },614  {615   "path": "nnunetv2/paths.py",616   "sha256": "b831a2b52fa22e8d33fecbd69ec47a0db150b4aa7226e6793672f46e9524d36e",617   "language": "Python",618   "lines": 39,619   "truncated": false,620   "block": 3,621   "row": 20005622  },623  {624   "path": "nnunetv2/postprocessing/remove_connected_components.py",625   "sha256": "27404334a6c26a5cf2cfe38543c12e2902f62ad46207abb6d83a55dfe1050db9",626   "language": "Python",627   "lines": 362,628   "truncated": false,629   "block": 12,630   "row": 20866631  },632  {633   "path": "nnunetv2/preprocessing/cropping/cropping.py",634   "sha256": "1aa68a6307f9d1549f18070ab461865ff38131d9dffdae7c855938f2b9581f64",635   "language": "Python",636   "lines": 43,637   "truncated": false,638   "block": 17,639   "row": 20962640  },641  {642   "path": "nnunetv2/preprocessing/normalization/default_normalization_schemes.py",643   "sha256": "d8487e191523194d19b74f76b831605333de0332a3b80184991dd2eac2493664",644   "language": "Python",645   "lines": 98,646   "truncated": false,647   "block": 3,648   "row": 22317649  },650  {651   "path": "nnunetv2/preprocessing/normalization/map_channel_name_to_normalization.py",652   "sha256": "e195bc1f5cdfcf723b1a11c15e2539f15d11018bfcf20a758e18badca4b723fb",653   "language": "Python",654   "lines": 24,655   "truncated": false,656   "block": 1,657   "row": 5693658  },659  {660   "path": "nnunetv2/preprocessing/preprocessors/default_preprocessor.py",661   "sha256": "ac7b85e61bf452def9d1b1ba2d827255be2696972955cd6613ace972ada85a8c",662   "language": "Python",663   "lines": 297,664   "truncated": false,665   "block": 18,666   "row": 2539667  },668  {669   "path": "nnunetv2/preprocessing/resampling/default_resampling.py",670   "sha256": "dd19a74ad7fe9d45baeb6de686746fe31b76475e17fc64fed9f9b7fb0ac93428",671   "language": "Python",672   "lines": 216,673   "truncated": false,674   "block": 17,675   "row": 32594676  },677  {678   "path": "nnunetv2/preprocessing/resampling/utils.py",679   "sha256": "7f5cceddb94a028944f64074af41dc202d3ecba56e5c08dc7e2022e16ee1d141",680   "language": "Python",681   "lines": 15,682   "truncated": false,683   "block": 1,684   "row": 5530685  },686  {687   "path": "nnunetv2/run/load_pretrained_weights.py",688   "sha256": "b129310bb20d220748cf4b939d48b5348f9e29761a805a89c5c4348ac75ff587",689   "language": "Python",690   "lines": 70,691   "truncated": false,692   "block": 12,693   "row": 11072694  },695  {696   "path": "nnunetv2/run/run_training.py",697   "sha256": "04f9bc45a703f1446a27ac5e00516e47467d974f462b1e1e9a6a02205b255878",698   "language": "Python",699   "lines": 280,700   "truncated": false,701   "block": 18,702   "row": 1957703  },704  {705   "path": "nnunetv2/setup.py",706   "sha256": "105090a181d2b5356ef8712a44c2a949ab34ce8fbd67e01b5aafb6fb1911a15f",707   "language": "Python",708   "lines": 4,709   "truncated": false,710   "block": 1,711   "row": 5038712  },713  {714   "path": "nnunetv2/tests/integration_tests/add_lowres_and_cascade.py",715   "sha256": "c68d3e304e5cbedc3c3f3bea133ab6a6988048e5d5a0d888cfcf2847dfc3d340",716   "language": "Python",717   "lines": 33,718   "truncated": false,719   "block": 3,720   "row": 19614721  },722  {723   "path": "nnunetv2/tests/integration_tests/cleanup_integration_test.py",724   "sha256": "5e0dbbdb89a7a61883dcf1f0147c52e11aabb9b79e552567170ce6a3ff1e9a68",725   "language": "Python",726   "lines": 19,727   "truncated": false,728   "block": 3,729   "row": 18562730  },731  {732   "path": "nnunetv2/tests/integration_tests/lsf_commands.sh",733   "sha256": "9b23242ed31e56c2b50b589be48c08008f2292f5863f8e78802d6bb637e16d37",734   "language": "Shell",735   "lines": 10,736   "truncated": false,737   "block": 1,738   "row": 11670739  },740  {741   "path": "nnunetv2/tests/integration_tests/prepare_integration_tests.sh",742   "sha256": "5362b5a197cb6fa44b4c3af16d0c37d8773cfc9f4a0fc78d6cf801d495b47cca",743   "language": "Shell",744   "lines": 18,745   "truncated": false,746   "block": 4,747   "row": 1721748  },749  {750   "path": "nnunetv2/tests/integration_tests/run_integration_test.sh",751   "sha256": "b8ffbc76c8d257a8068e4d830fe6fba146848cd4d9c8d709230674342a995807",752   "language": "Shell",753   "lines": 27,754   "truncated": false,755   "block": 4,756   "row": 1827757  },758  {759   "path": "nnunetv2/tests/integration_tests/run_integration_test_bestconfig_inference.py",760   "sha256": "acfbfba79a943003d1d40b0c140f2790b17948dcac2f4cb322a43f253d93609e",761   "language": "Python",762   "lines": 75,763   "truncated": false,764   "block": 1,765   "row": 7223766  },767  {768   "path": "nnunetv2/tests/integration_tests/run_integration_test_trainingOnly_DDP.sh",769   "sha256": "99494db232e67bf1ef81046125863228612151df87c3221cad0372679e294f2a",770   "language": "Shell",771   "lines": 1,772   "truncated": false,773   "block": 1,774   "row": 11108775  },776  {777   "path": "nnunetv2/training/data_augmentation/compute_initial_patch_size.py",778   "sha256": "4da8a4fbb4db5bd5a428a596793c0bd685d360ec8b24bd4be7495fda59352e9f",779   "language": "Python",780   "lines": 24,781   "truncated": false,782   "block": 1,783   "row": 5807784  },785  {786   "path": "nnunetv2/training/data_augmentation/custom_transforms/cascade_transforms.py",787   "sha256": "246f051c507492f6861ae505535b13fa1e2172f13e4407364212df2c8d8ae2e7",788   "language": "Python",789   "lines": 136,790   "truncated": false,791   "block": 1,792   "row": 8024793  },794  {795   "path": "nnunetv2/training/data_augmentation/custom_transforms/deep_supervision_donwsampling.py",796   "sha256": "f2f85b8a092e4fee07b1c6763dd44566592a1a780a74cec20f7e877fb1d4ba9b",797   "language": "Python",798   "lines": 55,799   "truncated": false,800   "block": 1,801   "row": 6577802  },803  {804   "path": "nnunetv2/training/data_augmentation/custom_transforms/limited_length_multithreaded_augmenter.py",805   "sha256": "d0b90b227ff4d1a9640e0220307484d4b7bab7e6ebc7483d5449d120ab95d68a",806   "language": "Python",807   "lines": 10,808   "truncated": false,809   "block": 3,810   "row": 17962811  },812  {813   "path": "nnunetv2/training/data_augmentation/custom_transforms/manipulating_data_dict.py",814   "sha256": "ac4bfae716874c7ec82a4d2fb989cbf47205482e0edb5ac2f64105ccce937697",815   "language": "Python",816   "lines": 10,817   "truncated": false,818   "block": 3,819   "row": 17897820  },821  {822   "path": "nnunetv2/training/data_augmentation/custom_transforms/masking.py",823   "sha256": "e0a648d7875ae44c17ffb9af200ab0e1dab263c4f29678075db7a6819a243031",824   "language": "Python",825   "lines": 22,826   "truncated": false,827   "block": 1,828   "row": 5650829  },830  {831   "path": "nnunetv2/training/data_augmentation/custom_transforms/region_based_training.py",832   "sha256": "5b13716e7aaa8e49b8a325da52d8ad343b2e8e8cc2a01d40a6d005ce9e6e6914",833   "language": "Python",834   "lines": 38,835   "truncated": false,836   "block": 3,837   "row": 19773838  },839  {840   "path": "nnunetv2/training/data_augmentation/custom_transforms/transforms_for_dummy_2d.py",841   "sha256": "63443f7e76981ee4eed59649ab8b6cef09bddd63da8d9ccace5d836afb82532f",842   "language": "Python",843   "lines": 45,844   "truncated": false,845   "block": 1,846   "row": 6496847  },848  {849   "path": "nnunetv2/training/dataloading/base_data_loader.py",850   "sha256": "a53e8a77263185df3630961b7fbf3ee47744abf391228e3ee88d3cffdee4d785",851   "language": "Python",852   "lines": 138,853   "truncated": false,854   "block": 17,855   "row": 31635856  },857  {858   "path": "nnunetv2/training/dataloading/data_loader_2d.py",859   "sha256": "051374940624400aaa0271f698ce57a6a6c4b4b413411d0470661b613e464e60",860   "language": "Python",861   "lines": 94,862   "truncated": false,863   "block": 3,864   "row": 23363865  },866  {867   "path": "nnunetv2/training/dataloading/data_loader_3d.py",868   "sha256": "917de37e1598ec4ef9a7052526fa7217cb85e4180581ca04d69144457d3622fc",869   "language": "Python",870   "lines": 57,871   "truncated": false,872   "block": 17,873   "row": 25180874  },875  {876   "path": "nnunetv2/training/dataloading/nnunet_dataset.py",877   "sha256": "1f7d8857d094e7ed809ccd26491d42b496014df9aa07efb07b9ce212a1006ba7",878   "language": "Python",879   "lines": 146,880   "truncated": false,881   "block": 3,882   "row": 23838883  },884  {885   "path": "nnunetv2/training/dataloading/utils.py",886   "sha256": "15f56b0352439b447e923ed81103e36b98141a029a467907c4cf3db9c516c884",887   "language": "Python",888   "lines": 82,889   "truncated": false,890   "block": 12,891   "row": 11172892  },893  {894   "path": "nnunetv2/training/logging/nnunet_logger.py",895   "sha256": "ed79dabcd02fab19fe934df9c01c0d41fe9d41cd910c504b9061ebc49dd963a2",896   "language": "Python",897   "lines": 103,898   "truncated": false,899   "block": 3,900   "row": 22730901  },902  {903   "path": "nnunetv2/training/loss/compound_losses.py",904   "sha256": "eeaf3a4e720a1737a81e8750f181a36911203a6c4f87d7f515fad3c6511bd5b5",905   "language": "Python",906   "lines": 150,907   "truncated": false,908   "block": 6,909   "row": 43214910  },911  {912   "path": "nnunetv2/training/loss/deep_supervision.py",913   "sha256": "7ecf90c7f2b9cf731dc6eddd85ad562c5e9be73f02e2724f2db8a40011751e3f",914   "language": "Python",915   "lines": 30,916   "truncated": false,917   "block": 6,918   "row": 28384919  },920  {921   "path": "nnunetv2/training/loss/dice.py",922   "sha256": "d175111b86647e840641cb4f65ea6bd9b49aa81f64c73637c2dbf84b709dbe91",923   "language": "Python",924   "lines": 192,925   "truncated": false,926   "block": 6,927   "row": 44466928  },929  {930   "path": "nnunetv2/training/loss/robust_ce_loss.py",931   "sha256": "d0f74c94846f03d19658c01c429260ca18c0d7bd2fcc59dab61c82d8d588acaa",932   "language": "Python",933   "lines": 32,934   "truncated": false,935   "block": 1,936   "row": 5805937  },938  {939   "path": "nnunetv2/training/lr_scheduler/polylr.py",940   "sha256": "b58eb2d83c0f3c6c72503d7d65870e888937321e3b2fc86266e92236d232e923",941   "language": "Python",942   "lines": 20,943   "truncated": false,944   "block": 3,945   "row": 18749946  },947  {948   "path": "nnunetv2/training/nnUNetTrainer/my_nnUNetTrainer_GOUHFI.py",949   "sha256": "8b9717c6cb3d0f44c7fd557606c70c2f82f61781cddd880cb1e035fec7896881",950   "language": "Python",951   "lines": 116,952   "truncated": false,953   "block": 17,954   "row": 28336955  },956  {957   "path": "nnunetv2/training/nnUNetTrainer/my_trainer_gouhfi_parc.py",958   "sha256": "05913ad17e99fe022499945e9d2326bf8398e286298bd129f1abd97fc8e8102d",959   "language": "Python",960   "lines": 111,961   "truncated": false,962   "block": 17,963   "row": 28263964  },965  {966   "path": "nnunetv2/training/nnUNetTrainer/nnUNetTrainer.py",967   "sha256": "6f7bd789e34836e24d49caa87ccf18b7bb31b93422121390ba75568ccc090b2d",968   "language": "Python",969   "lines": 1307,970   "truncated": false,971   "block": 18,972   "row": 5625973  },974  {975   "path": "nnunetv2/training/nnUNetTrainer/nnUNetTrainer_NoDA_500epochs_AdamW.py",976   "sha256": "024d57d1eef9a4d4520ccb0e29daac06e68cb32016c8bec66f9353a57ad7d710",977   "language": "Python",978   "lines": 53,979   "truncated": false,980   "block": 17,981   "row": 24201982  },983  {984   "path": "nnunetv2/training/nnUNetTrainer/variants/benchmarking/nnUNetTrainerBenchmark_5epochs.py",985   "sha256": "a73b15a3803c12d078a1064710cd88b70f8d12330ef2cf7b6655c7b2d569bcd8",986   "language": "Python",987   "lines": 65,988   "truncated": false,989   "block": 3,990   "row": 21095991  },992  {993   "path": "nnunetv2/training/nnUNetTrainer/variants/benchmarking/nnUNetTrainerBenchmark_5epochs_noDataLoading.py",994   "sha256": "5020fa1982e885b428c1aeea8dcdd817e9c80a3e91f0f808298e1a440a4b4e84",995   "language": "Python",996   "lines": 65,997   "truncated": false,998   "block": 6,999   "row": 343131000  },1001  {1002   "path": "nnunetv2/training/nnUNetTrainer/variants/data_augmentation/nnUNetTrainerDA5.py",1003   "sha256": "0d1e2c4ec3c06743f4c3ce1f6db57b81262ab853296727f862da586781788dfe",1004   "language": "Python",1005   "lines": 419,1006   "truncated": false,1007   "block": 7,1008   "row": 86351009  },1010  {1011   "path": "nnunetv2/training/nnUNetTrainer/variants/data_augmentation/nnUNetTrainerDAOrd0.py",1012   "sha256": "31860d6ad44feb06c5a49eed8303458a554bd16615054829f4ae4644c1439aff",1013   "language": "Python",1014   "lines": 157,1015   "truncated": false,1016   "block": 7,1017   "row": 17581018  },1019  {1020   "path": "nnunetv2/training/nnUNetTrainer/variants/data_augmentation/nnUNetTrainerNoDA.py",1021   "sha256": "393fd10571266f1a7dce4f43ded9aaf5b80f76e07264d1b7833d3985d4d1c4f0",1022   "language": "Python",1023   "lines": 40,1024   "truncated": false,1025   "block": 6,1026   "row": 323071027  },1028  {1029   "path": "nnunetv2/training/nnUNetTrainer/variants/data_augmentation/nnUNetTrainerNoMirroring.py",1030   "sha256": "cf53e995df971cea54d4a0c4771bee302fe329a586aa8861a345700c636e703e",1031   "language": "Python",1032   "lines": 28,1033   "truncated": false,1034   "block": 3,1035   "row": 192571036  },1037  {1038   "path": "nnunetv2/training/nnUNetTrainer/variants/loss/nnUNetTrainerCELoss.py",1039   "sha256": "96d9858ca55b3257553fe82717c71ce8b94a453007038eb8848ebd5baadf19b4",1040   "language": "Python",1041   "lines": 41,1042   "truncated": false,1043   "block": 6,1044   "row": 302841045  },1046  {1047   "path": "nnunetv2/training/nnUNetTrainer/variants/loss/nnUNetTrainerDiceLoss.py",1048   "sha256": "1d4b045166e8c1bc7a3718b9d92294f93b554a2a94e23da4eb474d8d8a05cda2",1049   "language": "Python",1050   "lines": 60,1051   "truncated": false,1052   "block": 3,1053   "row": 212951054  },1055  {1056   "path": "nnunetv2/training/nnUNetTrainer/variants/loss/nnUNetTrainerTopkLoss.py",1057   "sha256": "80f3b9684439165f4e5b3356ce554dedcfb2a3c2ccccd1e201f6460f3029cd78",1058   "language": "Python",1059   "lines": 76,1060   "truncated": false,1061   "block": 1,1062   "row": 69561063  },1064  {1065   "path": "nnunetv2/training/nnUNetTrainer/variants/lr_schedule/nnUNetTrainerCosAnneal.py",1066   "sha256": "a60db3062260a0bdfaab36e2f66eded0daab0766b4a384c0a97d9830fe007c52",1067   "language": "Python",1068   "lines": 13,1069   "truncated": false,1070   "block": 3,1071   "row": 183901072  },1073  {1074   "path": "nnunetv2/training/nnUNetTrainer/variants/network_architecture/nnUNetTrainerBN.py",1075   "sha256": "7a8fdd544b6192144674961407d799eb80faa1efe55df0f3b576faf4fd755e17",1076   "language": "Python",1077   "lines": 32,1078   "truncated": false,1079   "block": 3,1080   "row": 198241081  },1082  {1083   "path": "nnunetv2/training/nnUNetTrainer/variants/network_architecture/nnUNetTrainerNoDeepSupervision.py",1084   "sha256": "3c52f646c39a6f0c8036e59d8589afc5479d106c77a15a0115badcf754a87cd8",1085   "language": "Python",1086   "lines": 16,1087   "truncated": false,1088   "block": 6,1089   "row": 227891090  },1091  {1092   "path": "nnunetv2/training/nnUNetTrainer/variants/optimizer/nnUNetTrainerAdam.py",1093   "sha256": "6d6c7eccce21ca33757752b21a363722cd68093fdb5aa1d40ac47a37678640b4",1094   "language": "Python",1095   "lines": 58,1096   "truncated": false,1097   "block": 3,1098   "row": 211171099  },1100  {1101   "path": "nnunetv2/training/nnUNetTrainer/variants/optimizer/nnUNetTrainerAdan.py",1102   "sha256": "bb5606a3a5b078f42e689156381c87d8ce5f0a24a18f827338ee807ee30b8f9a",1103   "language": "Python",1104   "lines": 66,1105   "truncated": false,1106   "block": 3,1107   "row": 215141108  },1109  {1110   "path": "nnunetv2/training/nnUNetTrainer/variants/sampling/nnUNetTrainer_probabilisticOversampling.py",1111   "sha256": "c1d93287be131a4cbc0f88b0ce9a1aecc49c64489a920d6a1137bf7a08828589",1112   "language": "Python",1113   "lines": 84,1114   "truncated": false,1115   "block": 6,1116   "row": 415131117  },1118  {1119   "path": "nnunetv2/training/nnUNetTrainer/variants/training_length/nnUNetTrainer_Xepochs.py",1120   "sha256": "2af082b38c1c5c4ab9dc97fc30011808d3e119e64ce53698cf736352b487f162",1121   "language": "Python",1122   "lines": 76,1123   "truncated": false,1124   "block": 3,1125   "row": 218921126  },1127  {1128   "path": "nnunetv2/training/nnUNetTrainer/variants/training_length/nnUNetTrainer_Xepochs_NoMirroring.py",1129   "sha256": "7f9a1ff6c03415c577a425187ddf74c45d85d793b4f79b8950fc8070640ae6ae",1130   "language": "Python",1131   "lines": 60,1132   "truncated": false,1133   "block": 3,1134   "row": 214031135  },1136  {1137   "path": "nnunetv2/utilities/collate_outputs.py",1138   "sha256": "f7363bce1b01e4be63b5b5ac215509ee67d5df9863ae0ac433bf2d4573228da0",1139   "language": "Python",1140   "lines": 24,1141   "truncated": false,1142   "block": 3,1143   "row": 188771144  },1145  {1146   "path": "nnunetv2/utilities/crossval_split.py",1147   "sha256": "2fcd9e124407c9782d155fe7254fa2c1eaadf6204db92d3461ed193f0def5728",1148   "language": "Python",1149   "lines": 16,1150   "truncated": false,1151   "block": 1,1152   "row": 54661153  },1154  {1155   "path": "nnunetv2/utilities/dataset_name_id_conversion.py",1156   "sha256": "2ef62f02c3027e95370f81dd1c0a0b0b4515b51efb05f0d1a68b6eeb367e91ff",1157   "language": "Python",1158   "lines": 74,1159   "truncated": false,1160   "block": 3,1161   "row": 220961162  },1163  {1164   "path": "nnunetv2/utilities/ddp_allgather.py",1165   "sha256": "b23c0b7cac223da285de80461873196e2e60c0e0ddce776f858cc4b0777059af",1166   "language": "Python",1167   "lines": 49,1168   "truncated": false,1169   "block": 3,1170   "row": 198721171  },1172  {1173   "path": "nnunetv2/utilities/default_n_proc_DA.py",1174   "sha256": "75f2c0661ac85456af867ccba53aac33bc1fddfb9a0bc3b5e6efe88e874403dc",1175   "language": "Python",1176   "lines": 44,1177   "truncated": false,1178   "block": 3,1179   "row": 199921180  },1181  {1182   "path": "nnunetv2/utilities/file_path_utilities.py",1183   "sha256": "c1d3501ea6a05b17cfde1666e714cd0dbbcec7710ceac43430474cc666170f42",1184   "language": "Python",1185   "lines": 123,1186   "truncated": false,1187   "block": 3,1188   "row": 233211189  },1190  {1191   "path": "nnunetv2/utilities/find_class_by_name.py",1192   "sha256": "7be2e0e9fc36de096f9da959a7146955e20dd298a4dcce8f7159c7c5ee65c3c5",1193   "language": "Python",1194   "lines": 24,1195   "truncated": false,1196   "block": 3,1197   "row": 188321198  },1199  {1200   "path": "nnunetv2/utilities/get_network_from_plans.py",

Showing the first 1,200 of 1290 lines. Download the file for the rest.