pytme 0.2.9.post1__cp311-cp311-macosx_15_0_arm64.whl → 0.3b0__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 (63) hide show
  1. pytme-0.2.9.post1.data/scripts/estimate_ram_usage.py → pytme-0.3b0.data/scripts/estimate_memory_usage.py +16 -33
  2. {pytme-0.2.9.post1.data → pytme-0.3b0.data}/scripts/match_template.py +224 -223
  3. {pytme-0.2.9.post1.data → pytme-0.3b0.data}/scripts/postprocess.py +283 -163
  4. {pytme-0.2.9.post1.data → pytme-0.3b0.data}/scripts/preprocess.py +11 -8
  5. {pytme-0.2.9.post1.data → pytme-0.3b0.data}/scripts/preprocessor_gui.py +10 -9
  6. {pytme-0.2.9.post1.dist-info → pytme-0.3b0.dist-info}/METADATA +10 -9
  7. {pytme-0.2.9.post1.dist-info → pytme-0.3b0.dist-info}/RECORD +61 -58
  8. {pytme-0.2.9.post1.dist-info → pytme-0.3b0.dist-info}/entry_points.txt +1 -1
  9. scripts/{estimate_ram_usage.py → estimate_memory_usage.py} +16 -33
  10. scripts/extract_candidates.py +224 -0
  11. scripts/match_template.py +224 -223
  12. scripts/postprocess.py +283 -163
  13. scripts/preprocess.py +11 -8
  14. scripts/preprocessor_gui.py +10 -9
  15. scripts/refine_matches.py +626 -0
  16. tests/preprocessing/test_frequency_filters.py +9 -4
  17. tests/test_analyzer.py +143 -138
  18. tests/test_matching_cli.py +85 -30
  19. tests/test_matching_exhaustive.py +1 -2
  20. tests/test_matching_optimization.py +4 -9
  21. tests/test_orientations.py +0 -1
  22. tme/__version__.py +1 -1
  23. tme/analyzer/__init__.py +2 -0
  24. tme/analyzer/_utils.py +25 -17
  25. tme/analyzer/aggregation.py +384 -220
  26. tme/analyzer/base.py +138 -0
  27. tme/analyzer/peaks.py +150 -91
  28. tme/analyzer/proxy.py +122 -0
  29. tme/backends/__init__.py +4 -3
  30. tme/backends/_cupy_utils.py +25 -24
  31. tme/backends/_jax_utils.py +4 -3
  32. tme/backends/cupy_backend.py +4 -13
  33. tme/backends/jax_backend.py +6 -8
  34. tme/backends/matching_backend.py +4 -3
  35. tme/backends/mlx_backend.py +4 -3
  36. tme/backends/npfftw_backend.py +7 -5
  37. tme/backends/pytorch_backend.py +14 -4
  38. tme/cli.py +126 -0
  39. tme/density.py +4 -3
  40. tme/filters/__init__.py +1 -1
  41. tme/filters/_utils.py +4 -3
  42. tme/filters/bandpass.py +6 -4
  43. tme/filters/compose.py +5 -4
  44. tme/filters/ctf.py +426 -214
  45. tme/filters/reconstruction.py +58 -28
  46. tme/filters/wedge.py +139 -61
  47. tme/filters/whitening.py +36 -36
  48. tme/matching_data.py +4 -3
  49. tme/matching_exhaustive.py +17 -16
  50. tme/matching_optimization.py +5 -4
  51. tme/matching_scores.py +4 -3
  52. tme/matching_utils.py +41 -3
  53. tme/memory.py +4 -3
  54. tme/orientations.py +9 -6
  55. tme/parser.py +5 -4
  56. tme/preprocessor.py +4 -3
  57. tme/rotations.py +10 -7
  58. tme/structure.py +4 -3
  59. tests/data/Maps/.DS_Store +0 -0
  60. tests/data/Structures/.DS_Store +0 -0
  61. {pytme-0.2.9.post1.dist-info → pytme-0.3b0.dist-info}/WHEEL +0 -0
  62. {pytme-0.2.9.post1.dist-info → pytme-0.3b0.dist-info}/licenses/LICENSE +0 -0
  63. {pytme-0.2.9.post1.dist-info → pytme-0.3b0.dist-info}/top_level.txt +0 -0
tme/analyzer/_utils.py CHANGED
@@ -1,8 +1,9 @@
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- """ Analyzer utility functions.
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+ """
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+ Analyzer utility functions.
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- Copyright (c) 2023-2025 European Molecular Biology Laboratory
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+ Copyright (c) 2023-2025 European Molecular Biology Laboratory
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- Author: Valentin Maurer <valentin.maurer@embl-hamburg.de>
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+ Author: Valentin Maurer <valentin.maurer@embl-hamburg.de>
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  """
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  from typing import Tuple
@@ -161,26 +162,33 @@ def score_to_cart(
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  targetshape = be.to_backend_array(targetshape)
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  templateshape = be.to_backend_array(templateshape)
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164
 
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+ valid_positions = be.ones((positions.shape[0],)) == 1
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+
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  # Wrap peaks around score space
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  if fourier_shift is not None:
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  fourier_shift = be.to_backend_array(fourier_shift)
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  positions = be.add(positions, fourier_shift)
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  positions = be.mod(positions, fast_shape)
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172
 
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- output_shape = _convmode_to_shape(
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- convolution_mode=convolution_mode,
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- targetshape=targetshape,
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- templateshape=templateshape,
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- convolution_shape=convolution_shape,
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- )
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- starts = be.astype(
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- be.divide(be.subtract(convolution_shape, output_shape), 2),
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- be._int_dtype,
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- )
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- stops = be.add(starts, output_shape)
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+ if convolution_mode is not None:
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+ output_shape = _convmode_to_shape(
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+ convolution_mode=convolution_mode,
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+ targetshape=targetshape,
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+ templateshape=templateshape,
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+ convolution_shape=convolution_shape,
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+ )
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+ starts = be.astype(
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+ be.divide(be.subtract(convolution_shape, output_shape), 2),
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+ be._int_dtype,
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+ )
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+ stops = be.add(starts, output_shape)
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185
 
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- valid_positions = be.multiply(positions >= starts, positions < stops)
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- valid_positions = be.sum(valid_positions, axis=1) == positions.shape[1]
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- positions = be.subtract(positions, starts)
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+ valid_positions = be.multiply(positions >= starts, positions < stops)
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+ valid_positions = be.sum(valid_positions, axis=1) == positions.shape[1]
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+ positions = be.subtract(positions, starts)
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189
 
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+ # Get rid of -1 position peaks used to keep GPU happy
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+ valid_positions = be.multiply(
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+ be.sum(positions >= 0, axis=1) == positions.shape[1], valid_positions
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+ )
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  return positions, valid_positions