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.
05.6k
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",