octopi 1.1__py3-none-any.whl → 1.2.0__py3-none-any.whl

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Files changed (45) hide show
  1. octopi/__init__.py +1 -0
  2. octopi/datasets/cached_datset.py +1 -1
  3. octopi/datasets/generators.py +1 -1
  4. octopi/datasets/io.py +200 -0
  5. octopi/datasets/multi_config_generator.py +1 -1
  6. octopi/entry_points/common.py +5 -5
  7. octopi/entry_points/create_slurm_submission.py +1 -1
  8. octopi/entry_points/run_create_targets.py +6 -6
  9. octopi/entry_points/run_evaluate.py +4 -3
  10. octopi/entry_points/run_extract_mb_picks.py +5 -5
  11. octopi/entry_points/run_localize.py +8 -9
  12. octopi/entry_points/run_optuna.py +7 -7
  13. octopi/entry_points/run_segment_predict.py +4 -4
  14. octopi/entry_points/run_train.py +7 -8
  15. octopi/extract/localize.py +11 -19
  16. octopi/extract/membranebound_extract.py +11 -10
  17. octopi/extract/midpoint_extract.py +3 -3
  18. octopi/models/common.py +1 -1
  19. octopi/processing/create_targets_from_picks.py +3 -4
  20. octopi/processing/evaluate.py +24 -11
  21. octopi/processing/importers.py +4 -4
  22. octopi/pytorch/hyper_search.py +2 -3
  23. octopi/pytorch/model_search_submitter.py +4 -4
  24. octopi/pytorch/segmentation.py +141 -190
  25. octopi/pytorch/segmentation_multigpu.py +162 -0
  26. octopi/pytorch/trainer.py +2 -2
  27. octopi/utils/__init__.py +0 -0
  28. octopi/utils/config.py +57 -0
  29. octopi/utils/io.py +128 -0
  30. octopi/{utils.py → utils/parsers.py} +10 -84
  31. octopi/{stopping_criteria.py → utils/stopping_criteria.py} +3 -3
  32. octopi/{visualization_tools.py → utils/visualization_tools.py} +4 -4
  33. octopi/workflows.py +236 -0
  34. {octopi-1.1.dist-info → octopi-1.2.0.dist-info}/METADATA +41 -29
  35. octopi-1.2.0.dist-info/RECORD +62 -0
  36. {octopi-1.1.dist-info → octopi-1.2.0.dist-info}/WHEEL +1 -1
  37. octopi-1.2.0.dist-info/entry_points.txt +3 -0
  38. {octopi-1.1.dist-info → octopi-1.2.0.dist-info/licenses}/LICENSE +3 -3
  39. octopi/io.py +0 -457
  40. octopi/processing/my_metrics.py +0 -26
  41. octopi/processing/writers.py +0 -102
  42. octopi-1.1.dist-info/RECORD +0 -59
  43. octopi-1.1.dist-info/entry_points.txt +0 -4
  44. /octopi/{losses.py → utils/losses.py} +0 -0
  45. /octopi/{submit_slurm.py → utils/submit_slurm.py} +0 -0
octopi-1.1.dist-info/RECORD DELETED
@@ -1,59 +0,0 @@
1
- octopi/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
2
- octopi/datasets/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
3
- octopi/datasets/augment.py,sha256=k7UXQzidPANaPuLoBzer_ZHc4_vF-kKTOyZisEnAbNw,3203
4
- octopi/datasets/cached_datset.py,sha256=eQgKjQ9Kz4RF5rs2saFE25p-YfspA24tq3-6ugukbRA,3909
5
- octopi/datasets/dataset.py,sha256=9C3AuD83FMswj4MYLFn5XPqvAP1a7MQSG7UNiStg090,511
6
- octopi/datasets/generators.py,sha256=aqsIhipkG6bBzwpUlvP_N5m2Je5vs4Vq7gQN1z2uKPc,18874
7
- octopi/datasets/mixup.py,sha256=BJUAmM7ItZWFChs8glnd8RNSXR5qGW7DHscbcVc3TsU,1575
8
- octopi/datasets/multi_config_generator.py,sha256=SIYqz3Xps4gyWgUo02W1KbObM4ye14dIHJi25XlIIRc,10805
9
- octopi/entry_points/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
10
- octopi/entry_points/common.py,sha256=o1H_rDkiflyOMkJr85aUgso31X4ib4wFAfqfh-CZqho,5351
11
- octopi/entry_points/create_slurm_submission.py,sha256=Fk9Bhn81SAf0SZW5ZkoOdV6afycw8aLk_tjkgYymEGk,8908
12
- octopi/entry_points/run_create_targets.py,sha256=IacDeL9k3sCRbeVuyn32IffjrdQe31VAbS4CxTWpHFk,11226
13
- octopi/entry_points/run_evaluate.py,sha256=I90kP_GOtAO7zbuEY9ptZ8Y-g1wZa41N9a2ZGbijEcs,2826
14
- octopi/entry_points/run_extract_mb_picks.py,sha256=8TFShlDUyFgDwFTmPeMyJPAMBsmuwNhG155d3bVaRgU,4854
15
- octopi/entry_points/run_extract_midpoint.py,sha256=O6GdkSD7oXIpSVqizOc6PHhv9nunz3j0RucmYQ2yryM,5742
16
- octopi/entry_points/run_localize.py,sha256=V_BhugnvvoTHf9mTZdQIbTLVKEwfGnuUAsykuGiSgkA,8233
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- octopi/entry_points/run_optuna.py,sha256=LQXQ6W3v8MhJ9EoKbtFc84Muy3ofjzo-0SyUQaMAaMs,5743
18
- octopi/entry_points/run_segment_predict.py,sha256=46CfxDWxbKAZT8o2xr4JiYAwLxVpxXLwGylZU8WXgMc,5442
19
- octopi/entry_points/run_train.py,sha256=zdeZxtwK0fJytex9TzZBXxpQxF8b3ljpWeYdBsuOR8k,8094
20
- octopi/extract/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
21
- octopi/extract/localize.py,sha256=7kPblW-Hzkxkrca4bEL0LJoAdKJTCL28lzzDhTGff3g,9815
22
- octopi/extract/membranebound_extract.py,sha256=VdlsiytoaKBk4wdhORJU8yRSOARFN2zvnF6PZpJkGmo,11208
23
- octopi/extract/midpoint_extract.py,sha256=W8sVIAweqkQcF18ie7tvvvOeBzRTBdH95FzPtjMcWjc,7033
24
- octopi/io.py,sha256=EuUTrLArNiErjB-ad0EWEljXcTcpNqEHqPS4goa495s,19565
25
- octopi/losses.py,sha256=fs9yR80Hs-hL07WgVMkRy5N81vzP5m9XBCvzO76bIPU,3097
26
- octopi/main.py,sha256=ef_zpvopl6JiN4gOT_x2QghRJriqg4iwRzBnvuiBeTo,4864
27
- octopi/models/AttentionUnet.py,sha256=r185aXRtfXhN-n8FxA-Sjz18nqpxHH_2t2uadrH-Mgs,1991
28
- octopi/models/MedNeXt.py,sha256=9q0FsyrqTx211hCbDv0Lm2XflzXL_bGA4-76BscziGk,4875
29
- octopi/models/ModelTemplate.py,sha256=X80EOXwSovCjmVb7x-0_JmRjHfDfLByDdd60MrgFTyw,1084
30
- octopi/models/SegResNet.py,sha256=1dK8dy_7hHHKYZLsTYafl__7MxQOlWGbBqQWPGxHSXg,3609
31
- octopi/models/Unet.py,sha256=7RGT_nl7ogsNlS3Y3Qexe305Ym9NlK9CV0y45g2DEU4,2171
32
- octopi/models/UnetPlusPlus.py,sha256=fnV-SvJV8B432KJXQAtdwLy8Va6DJ4fRB_7a1mZiqTU,1529
33
- octopi/models/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
34
- octopi/models/common.py,sha256=kXE0GcQSdfbiP0PDaJBkAJClBqTqCamP-2bHkbe0uBg,2307
35
- octopi/processing/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
36
- octopi/processing/create_targets_from_picks.py,sha256=wcCUCbw_fbSZuOIR32TgrADPHVDuH4RTdmiSTR_aDUw,4400
37
- octopi/processing/downsample.py,sha256=u3V2HULdKTLEthzI-MqJmI-NqpiyX0Vg61i77-j2MKQ,5392
38
- octopi/processing/evaluate.py,sha256=0w1iqmD8EXRdce-ctSoEJu5lAwYk1CjL4Qd_dpZt7Yw,13364
39
- octopi/processing/importers.py,sha256=TBgPlleGGOW8tJJLArrAFWxzvxH1qE-id_PTLRscgEs,8876
40
- octopi/processing/my_metrics.py,sha256=7ZhCEiSYkqbSpoTntAkCrr7y83u6-jI8k8d3P9TlrQA,1040
41
- octopi/processing/segmentation_from_picks.py,sha256=jah1gAXEn09LIok1Cb8IeVN-fT3jktcVPfjbOFHkgg0,7089
42
- octopi/processing/writers.py,sha256=YB6-0mwJ9sc_eJ3G_WItcqlBjFOpggyNhoRswKOZA6Q,3301
43
- octopi/pytorch/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
44
- octopi/pytorch/hyper_search.py,sha256=xCJ_8qYaK80UMb2JrBvU31tEZ8-L7MBGBE9pb63-8a0,9431
45
- octopi/pytorch/model_search_submitter.py,sha256=gpXI5RtXwC3T3wvAERWl0GNuhTGvzqW2guG6podgw6A,11247
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- octopi/pytorch/segmentation.py,sha256=1EWkOUb419U3Wwhxzc7L3BKUqH4NbzAW8othqT44TqA,14063
47
- octopi/pytorch/trainer.py,sha256=VLDp1hiCKC_l1YfNFcnTx8alKjXggpXRTo-ZtjhLoSg,17748
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- octopi/pytorch_lightning/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
49
- octopi/pytorch_lightning/optuna_pl_ddp.py,sha256=ynD5i81IP-awr6OD9GDurjrQK-5Kc079qPaukphTHnA,11924
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- octopi/pytorch_lightning/train_pl.py,sha256=igOHzU_mUdZRQGhoOGW5vmxJcHFcw5fAPHfVCIZ0eG4,10220
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- octopi/stopping_criteria.py,sha256=Fib1fiFqPQPLDxZQNUTgQInY8RWGNBzXkpqF_WJ2PSo,6112
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- octopi/submit_slurm.py,sha256=cRbJTESbPFCt6Cq4Hat2uPOQKFYMPcQxuNs0jc1ygUA,1945
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- octopi/utils.py,sha256=iezl5ui2E_Qs00_HS4uPPh008pdyY6IXI9euLfkUq4s,9008
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- octopi/visualization_tools.py,sha256=80Kj8yX09LEXJe3QqeithhlwEdoz9wOYRk7T1RFRmw4,7368
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- octopi-1.1.dist-info/LICENSE,sha256=zYaYdrEn2O4KTO8sLySIhHOKerzA69toCj2ywuvHT7Q,1816
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- octopi-1.1.dist-info/METADATA,sha256=8G-sdRk50HjWdu4Y_2alWs95IQYQvTiFPcn0EvkqdtA,4270
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- octopi-1.1.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
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- octopi-1.1.dist-info/entry_points.txt,sha256=FnDGURPvbr2Hl7n0LPN-5jHtvrKA87MNvhCFO-BwAfg,87
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- octopi-1.1.dist-info/RECORD,,
octopi-1.1.dist-info/entry_points.txt DELETED
@@ -1,4 +0,0 @@
1
- [console_scripts]
2
- octopi=octopi.main:cli_main
3
- octopi-slurm=octopi.main:cli_slurm_main
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-
/octopi/{losses.py → utils/losses.py} RENAMED
File without changes
/octopi/{submit_slurm.py → utils/submit_slurm.py} RENAMED
File without changes