pytme 0.3.1.post1__cp311-cp311-macosx_15_0_arm64.whl → 0.3.2.dev0__cp311-cp311-macosx_15_0_arm64.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (69) hide show
  1. pytme-0.3.2.dev0.data/scripts/estimate_ram_usage.py +97 -0
  2. {pytme-0.3.1.post1.data → pytme-0.3.2.dev0.data}/scripts/match_template.py +213 -196
  3. {pytme-0.3.1.post1.data → pytme-0.3.2.dev0.data}/scripts/postprocess.py +40 -78
  4. {pytme-0.3.1.post1.data → pytme-0.3.2.dev0.data}/scripts/preprocess.py +4 -5
  5. {pytme-0.3.1.post1.data → pytme-0.3.2.dev0.data}/scripts/preprocessor_gui.py +50 -103
  6. {pytme-0.3.1.post1.data → pytme-0.3.2.dev0.data}/scripts/pytme_runner.py +46 -69
  7. {pytme-0.3.1.post1.dist-info → pytme-0.3.2.dev0.dist-info}/METADATA +2 -1
  8. pytme-0.3.2.dev0.dist-info/RECORD +136 -0
  9. scripts/estimate_ram_usage.py +97 -0
  10. scripts/match_template.py +213 -196
  11. scripts/match_template_devel.py +1339 -0
  12. scripts/postprocess.py +40 -78
  13. scripts/preprocess.py +4 -5
  14. scripts/preprocessor_gui.py +50 -103
  15. scripts/pytme_runner.py +46 -69
  16. scripts/refine_matches.py +5 -7
  17. tests/preprocessing/test_compose.py +31 -30
  18. tests/preprocessing/test_frequency_filters.py +17 -32
  19. tests/preprocessing/test_preprocessor.py +0 -19
  20. tests/preprocessing/test_utils.py +13 -1
  21. tests/test_analyzer.py +2 -10
  22. tests/test_backends.py +47 -18
  23. tests/test_density.py +72 -13
  24. tests/test_extensions.py +1 -0
  25. tests/test_matching_cli.py +23 -9
  26. tests/test_matching_exhaustive.py +5 -5
  27. tests/test_matching_utils.py +3 -3
  28. tests/test_rotations.py +13 -23
  29. tests/test_structure.py +1 -7
  30. tme/__version__.py +1 -1
  31. tme/analyzer/aggregation.py +47 -16
  32. tme/analyzer/base.py +34 -0
  33. tme/analyzer/peaks.py +26 -13
  34. tme/analyzer/proxy.py +14 -0
  35. tme/backends/_jax_utils.py +124 -71
  36. tme/backends/cupy_backend.py +6 -19
  37. tme/backends/jax_backend.py +110 -105
  38. tme/backends/matching_backend.py +0 -17
  39. tme/backends/mlx_backend.py +0 -29
  40. tme/backends/npfftw_backend.py +100 -97
  41. tme/backends/pytorch_backend.py +65 -78
  42. tme/cli.py +2 -2
  43. tme/density.py +102 -58
  44. tme/extensions.cpython-311-darwin.so +0 -0
  45. tme/filters/_utils.py +52 -24
  46. tme/filters/bandpass.py +99 -105
  47. tme/filters/compose.py +133 -39
  48. tme/filters/ctf.py +51 -102
  49. tme/filters/reconstruction.py +67 -122
  50. tme/filters/wedge.py +296 -325
  51. tme/filters/whitening.py +39 -75
  52. tme/mask.py +2 -2
  53. tme/matching_data.py +87 -15
  54. tme/matching_exhaustive.py +70 -120
  55. tme/matching_optimization.py +9 -63
  56. tme/matching_scores.py +261 -100
  57. tme/matching_utils.py +150 -91
  58. tme/memory.py +1 -0
  59. tme/orientations.py +28 -8
  60. tme/preprocessor.py +0 -239
  61. tme/rotations.py +102 -70
  62. tme/structure.py +601 -631
  63. tme/types.py +1 -0
  64. pytme-0.3.1.post1.dist-info/RECORD +0 -133
  65. {pytme-0.3.1.post1.data → pytme-0.3.2.dev0.data}/scripts/estimate_memory_usage.py +0 -0
  66. {pytme-0.3.1.post1.dist-info → pytme-0.3.2.dev0.dist-info}/WHEEL +0 -0
  67. {pytme-0.3.1.post1.dist-info → pytme-0.3.2.dev0.dist-info}/entry_points.txt +0 -0
  68. {pytme-0.3.1.post1.dist-info → pytme-0.3.2.dev0.dist-info}/licenses/LICENSE +0 -0
  69. {pytme-0.3.1.post1.dist-info → pytme-0.3.2.dev0.dist-info}/top_level.txt +0 -0
tme/types.py CHANGED
@@ -3,6 +3,7 @@ from typing import Union, TypeVar, Tuple
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  BackendArray = TypeVar("backend_array")
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  NDArray = TypeVar("numpy.ndarray")
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  CupyArray = TypeVar("cupy.ndarray")
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+ JaxArray = TypeVar("jaxlib._jax.ArrayImpl")
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  TorchTensor = TypeVar("torch.Tensor")
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  MlxArray = TypeVar("mlx.core.array")
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  ArrayLike = TypeVar("array_like")
pytme-0.3.1.post1.dist-info/RECORD DELETED
@@ -1,133 +0,0 @@
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- scripts/eval.py,sha256=ebJVLxbRlB6TI5YHNr0VavZ4lmaRdf8QVafyiDhh_oU,2528
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- scripts/extract_candidates.py,sha256=B2O4Xm0eVJzBZOblfkH5za8fTxLIdBRDl89Qwkq4Kjk,8097
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- scripts/refine_matches.py,sha256=1AG-E2PuTauflR_qVC1CaZKg7ev9xxGu3CIYeyJ2-WQ,12777
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- tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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- tests/test_density.py,sha256=JVQunV445qij5WdcpKn-5GKqT3endzjXvBPkIaXPADo,18914
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- tests/test_matching_memory.py,sha256=XrBGRi4cIp3-4nN6s7tj0pBbFJrvJaG3vQdtK-6uzY0,1151
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- tests/test_matching_optimization.py,sha256=bYt3d_nHewTRxKCXgGaMLhObkqBufGwrYL4gfinr_jE,7732
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- tests/test_matching_utils.py,sha256=m6mkjo-rgA0q67MYQwjeyy_y6GBErh68A-lqxvQ8NT4,4948
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