pytme 0.3.1.post1__tar.gz → 0.3.2.dev0__tar.gz

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 (134) hide show
  1. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/PKG-INFO +2 -1
  2. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/pyproject.toml +3 -2
  3. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/pytme.egg-info/SOURCES.txt +0 -4
  4. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/scripts/match_template.py +213 -196
  5. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/scripts/postprocess.py +40 -78
  6. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/scripts/preprocess.py +4 -5
  7. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/scripts/preprocessor_gui.py +50 -103
  8. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/scripts/pytme_runner.py +46 -69
  9. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/scripts/refine_matches.py +5 -7
  10. pytme-0.3.2.dev0/tests/preprocessing/test_compose.py +77 -0
  11. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tests/preprocessing/test_frequency_filters.py +17 -32
  12. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tests/preprocessing/test_preprocessor.py +0 -19
  13. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tests/preprocessing/test_utils.py +13 -1
  14. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tests/test_analyzer.py +2 -10
  15. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tests/test_backends.py +47 -18
  16. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tests/test_density.py +72 -13
  17. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tests/test_extensions.py +1 -0
  18. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tests/test_matching_cli.py +23 -9
  19. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tests/test_matching_exhaustive.py +5 -5
  20. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tests/test_matching_utils.py +3 -3
  21. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tests/test_rotations.py +13 -23
  22. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tests/test_structure.py +1 -7
  23. pytme-0.3.2.dev0/tme/__version__.py +1 -0
  24. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/analyzer/aggregation.py +47 -16
  25. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/analyzer/base.py +34 -0
  26. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/analyzer/peaks.py +26 -13
  27. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/analyzer/proxy.py +14 -0
  28. pytme-0.3.2.dev0/tme/backends/_jax_utils.py +256 -0
  29. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/backends/cupy_backend.py +6 -19
  30. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/backends/jax_backend.py +110 -105
  31. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/backends/matching_backend.py +0 -17
  32. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/backends/mlx_backend.py +0 -29
  33. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/backends/npfftw_backend.py +100 -97
  34. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/backends/pytorch_backend.py +65 -78
  35. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/cli.py +2 -2
  36. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/density.py +102 -58
  37. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/filters/_utils.py +52 -24
  38. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/filters/bandpass.py +99 -105
  39. pytme-0.3.2.dev0/tme/filters/compose.py +176 -0
  40. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/filters/ctf.py +51 -102
  41. pytme-0.3.2.dev0/tme/filters/reconstruction.py +164 -0
  42. pytme-0.3.2.dev0/tme/filters/wedge.py +577 -0
  43. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/filters/whitening.py +39 -75
  44. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/mask.py +2 -2
  45. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/matching_data.py +87 -15
  46. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/matching_exhaustive.py +70 -120
  47. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/matching_optimization.py +9 -63
  48. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/matching_scores.py +261 -100
  49. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/matching_utils.py +150 -91
  50. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/memory.py +1 -0
  51. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/orientations.py +28 -8
  52. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/preprocessor.py +0 -239
  53. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/rotations.py +102 -70
  54. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/structure.py +601 -631
  55. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/types.py +1 -0
  56. pytme-0.3.1.post1/tests/data/Maps/emd_8621.mrc.gz +0 -0
  57. pytme-0.3.1.post1/tests/data/Structures/.DS_Store +0 -0
  58. pytme-0.3.1.post1/tests/data/Structures/5uz4.cif +0 -70548
  59. pytme-0.3.1.post1/tests/preprocessing/test_compose.py +0 -76
  60. pytme-0.3.1.post1/tme/__version__.py +0 -1
  61. pytme-0.3.1.post1/tme/backends/_cupy_utils.py +0 -735
  62. pytme-0.3.1.post1/tme/backends/_jax_utils.py +0 -203
  63. pytme-0.3.1.post1/tme/filters/compose.py +0 -82
  64. pytme-0.3.1.post1/tme/filters/reconstruction.py +0 -219
  65. pytme-0.3.1.post1/tme/filters/wedge.py +0 -606
  66. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/LICENSE +0 -0
  67. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/MANIFEST.in +0 -0
  68. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/README.md +0 -0
  69. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/scripts/__init__.py +0 -0
  70. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/scripts/estimate_memory_usage.py +0 -0
  71. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/scripts/eval.py +0 -0
  72. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/scripts/extract_candidates.py +0 -0
  73. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/scripts/match_template_filters.py +0 -0
  74. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/setup.cfg +0 -0
  75. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/setup.py +0 -0
  76. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tests/__init__.py +0 -0
  77. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tests/data/.DS_Store +0 -0
  78. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tests/data/Blurring/.DS_Store +0 -0
  79. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tests/data/Blurring/blob_width18.npy +0 -0
  80. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tests/data/Blurring/edgegaussian_sigma3.npy +0 -0
  81. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tests/data/Blurring/gaussian_sigma2.npy +0 -0
  82. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tests/data/Blurring/hamming_width6.npy +0 -0
  83. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tests/data/Blurring/kaiserb_width18.npy +0 -0
  84. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tests/data/Blurring/localgaussian_sigma0510.npy +0 -0
  85. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tests/data/Blurring/mean_size5.npy +0 -0
  86. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tests/data/Blurring/ntree_sigma0510.npy +0 -0
  87. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tests/data/Blurring/rank_rank3.npy +0 -0
  88. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tests/data/README.md +0 -0
  89. {pytme-0.3.1.post1/tests/data/Maps → pytme-0.3.2.dev0/tests/data/Raw}/.DS_Store +0 -0
  90. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tests/data/Raw/em_map.map +0 -0
  91. {pytme-0.3.1.post1/tests/data/Raw → pytme-0.3.2.dev0/tests/data/Structures}/.DS_Store +0 -0
  92. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tests/data/Structures/1pdj.cif +0 -0
  93. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tests/data/Structures/1pdj.pdb +0 -0
  94. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tests/data/Structures/5khe.cif +0 -0
  95. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tests/data/Structures/5khe.ent +0 -0
  96. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tests/data/Structures/5khe.pdb +0 -0
  97. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tests/preprocessing/__init__.py +0 -0
  98. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tests/test_matching_data.py +0 -0
  99. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tests/test_matching_memory.py +0 -0
  100. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tests/test_matching_optimization.py +0 -0
  101. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tests/test_orientations.py +0 -0
  102. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tests/test_parser.py +0 -0
  103. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/__init__.py +0 -0
  104. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/analyzer/__init__.py +0 -0
  105. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/analyzer/_utils.py +0 -0
  106. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/backends/__init__.py +0 -0
  107. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/backends/_numpyfftw_utils.py +0 -0
  108. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/data/__init__.py +0 -0
  109. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/data/c48n309.npy +0 -0
  110. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/data/c48n527.npy +0 -0
  111. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/data/c48n9.npy +0 -0
  112. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/data/c48u1.npy +0 -0
  113. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/data/c48u1153.npy +0 -0
  114. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/data/c48u1201.npy +0 -0
  115. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/data/c48u1641.npy +0 -0
  116. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/data/c48u181.npy +0 -0
  117. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/data/c48u2219.npy +0 -0
  118. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/data/c48u27.npy +0 -0
  119. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/data/c48u2947.npy +0 -0
  120. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/data/c48u3733.npy +0 -0
  121. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/data/c48u4749.npy +0 -0
  122. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/data/c48u5879.npy +0 -0
  123. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/data/c48u7111.npy +0 -0
  124. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/data/c48u815.npy +0 -0
  125. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/data/c48u83.npy +0 -0
  126. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/data/c48u8649.npy +0 -0
  127. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/data/c600v.npy +0 -0
  128. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/data/c600vc.npy +0 -0
  129. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/data/metadata.yaml +0 -0
  130. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/data/quat_to_numpy.py +0 -0
  131. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/data/scattering_factors.pickle +0 -0
  132. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/external/bindings.cpp +0 -0
  133. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/filters/__init__.py +0 -0
  134. {pytme-0.3.1.post1 → pytme-0.3.2.dev0}/tme/parser.py +0 -0
{pytme-0.3.1.post1 → pytme-0.3.2.dev0}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: pytme
3
- Version: 0.3.1.post1
3
+ Version: 0.3.2.dev0
4
4
  Summary: Python Template Matching Engine
5
5
  Author: Valentin Maurer
6
6
  Author-email: Valentin Maurer <valentin.maurer@embl-hamburg.de>
@@ -24,6 +24,7 @@ Requires-Dist: psutil
24
24
  Requires-Dist: h5py
25
25
  Requires-Dist: importlib_resources
26
26
  Requires-Dist: joblib
27
+ Requires-Dist: pydantic
27
28
  Provides-Extra: cupy
28
29
  Requires-Dist: cupy-cuda12x>13.0.0; extra == "cupy"
29
30
  Requires-Dist: voltools; extra == "cupy"
{pytme-0.3.1.post1 → pytme-0.3.2.dev0}/pyproject.toml RENAMED
@@ -7,7 +7,7 @@ name="pytme"
7
7
  authors = [
8
8
  { name = "Valentin Maurer", email = "valentin.maurer@embl-hamburg.de" },
9
9
  ]
10
- version="0.3.1.post1"
10
+ version="0.3.2-dev.0"
11
11
  description="Python Template Matching Engine"
12
12
  readme="README.md"
13
13
  requires-python = ">=3.11"
@@ -24,7 +24,8 @@ dependencies=[
24
24
  "psutil",
25
25
  "h5py",
26
26
  "importlib_resources",
27
- "joblib"
27
+ "joblib",
28
+ "pydantic",
28
29
  ]
29
30
  license = "GPL-2.0-only"
30
31
  classifiers = [
{pytme-0.3.1.post1 → pytme-0.3.2.dev0}/pytme.egg-info/SOURCES.txt RENAMED
@@ -41,8 +41,6 @@ tests/data/Blurring/localgaussian_sigma0510.npy
41
41
  tests/data/Blurring/mean_size5.npy
42
42
  tests/data/Blurring/ntree_sigma0510.npy
43
43
  tests/data/Blurring/rank_rank3.npy
44
- tests/data/Maps/.DS_Store
45
- tests/data/Maps/emd_8621.mrc.gz
46
44
  tests/data/Raw/.DS_Store
47
45
  tests/data/Raw/em_map.map
48
46
  tests/data/Structures/.DS_Store
@@ -51,7 +49,6 @@ tests/data/Structures/1pdj.pdb
51
49
  tests/data/Structures/5khe.cif
52
50
  tests/data/Structures/5khe.ent
53
51
  tests/data/Structures/5khe.pdb
54
- tests/data/Structures/5uz4.cif
55
52
  tests/preprocessing/__init__.py
56
53
  tests/preprocessing/test_compose.py
57
54
  tests/preprocessing/test_frequency_filters.py
@@ -81,7 +78,6 @@ tme/analyzer/base.py
81
78
  tme/analyzer/peaks.py
82
79
  tme/analyzer/proxy.py
83
80
  tme/backends/__init__.py
84
- tme/backends/_cupy_utils.py
85
81
  tme/backends/_jax_utils.py
86
82
  tme/backends/_numpyfftw_utils.py
87
83
  tme/backends/cupy_backend.py