pytme 0.2.0b0__cp311-cp311-macosx_14_0_arm64.whl → 0.2.2__cp311-cp311-macosx_14_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 (52) hide show
  1. pytme-0.2.2.data/scripts/match_template.py +1187 -0
  2. {pytme-0.2.0b0.data → pytme-0.2.2.data}/scripts/postprocess.py +170 -71
  3. {pytme-0.2.0b0.data → pytme-0.2.2.data}/scripts/preprocessor_gui.py +179 -86
  4. pytme-0.2.2.dist-info/METADATA +91 -0
  5. pytme-0.2.2.dist-info/RECORD +74 -0
  6. {pytme-0.2.0b0.dist-info → pytme-0.2.2.dist-info}/WHEEL +1 -1
  7. scripts/extract_candidates.py +126 -87
  8. scripts/match_template.py +596 -209
  9. scripts/match_template_filters.py +571 -223
  10. scripts/postprocess.py +170 -71
  11. scripts/preprocessor_gui.py +179 -86
  12. scripts/refine_matches.py +567 -159
  13. tme/__init__.py +0 -1
  14. tme/__version__.py +1 -1
  15. tme/analyzer.py +627 -855
  16. tme/backends/__init__.py +41 -11
  17. tme/backends/_jax_utils.py +185 -0
  18. tme/backends/cupy_backend.py +120 -225
  19. tme/backends/jax_backend.py +282 -0
  20. tme/backends/matching_backend.py +464 -388
  21. tme/backends/mlx_backend.py +45 -68
  22. tme/backends/npfftw_backend.py +256 -514
  23. tme/backends/pytorch_backend.py +41 -154
  24. tme/density.py +312 -421
  25. tme/extensions.cpython-311-darwin.so +0 -0
  26. tme/matching_data.py +366 -303
  27. tme/matching_exhaustive.py +279 -1521
  28. tme/matching_optimization.py +234 -129
  29. tme/matching_scores.py +884 -0
  30. tme/matching_utils.py +281 -387
  31. tme/memory.py +377 -0
  32. tme/orientations.py +226 -66
  33. tme/parser.py +3 -4
  34. tme/preprocessing/__init__.py +2 -0
  35. tme/preprocessing/_utils.py +217 -0
  36. tme/preprocessing/composable_filter.py +31 -0
  37. tme/preprocessing/compose.py +55 -0
  38. tme/preprocessing/frequency_filters.py +388 -0
  39. tme/preprocessing/tilt_series.py +1011 -0
  40. tme/preprocessor.py +574 -530
  41. tme/structure.py +495 -189
  42. tme/types.py +5 -3
  43. pytme-0.2.0b0.data/scripts/match_template.py +0 -800
  44. pytme-0.2.0b0.dist-info/METADATA +0 -73
  45. pytme-0.2.0b0.dist-info/RECORD +0 -66
  46. tme/helpers.py +0 -881
  47. tme/matching_constrained.py +0 -195
  48. {pytme-0.2.0b0.data → pytme-0.2.2.data}/scripts/estimate_ram_usage.py +0 -0
  49. {pytme-0.2.0b0.data → pytme-0.2.2.data}/scripts/preprocess.py +0 -0
  50. {pytme-0.2.0b0.dist-info → pytme-0.2.2.dist-info}/LICENSE +0 -0
  51. {pytme-0.2.0b0.dist-info → pytme-0.2.2.dist-info}/entry_points.txt +0 -0
  52. {pytme-0.2.0b0.dist-info → pytme-0.2.2.dist-info}/top_level.txt +0 -0
@@ -1,73 +0,0 @@
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- Metadata-Version: 2.1
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- Name: pytme
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- Version: 0.2.0b0
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- Summary: Python Template Matching Engine
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- Author: Valentin Maurer
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- Author-email: Valentin Maurer <valentin.maurer@embl-hamburg.de>
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- License: Proprietary
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- Project-URL: Homepage, https://github.com/KosinskiLab/pyTME
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- Classifier: Programming Language :: Python :: 3
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- Classifier: Operating System :: OS Independent
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- Requires-Python: >=3.11
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- Description-Content-Type: text/markdown
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- License-File: LICENSE
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- Requires-Dist: mrcfile >=1.4.3
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- Requires-Dist: numpy >=1.22.2
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- Requires-Dist: pyfftw >=0.13.1
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- Requires-Dist: pytest >=6.2.5
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- Requires-Dist: PyWavelets >=1.2.0
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- Requires-Dist: PyYAML >=6.0
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- Requires-Dist: scikit-image >=0.19.0
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- Requires-Dist: scikit-learn >=1.2.1
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- Requires-Dist: scipy >=1.9.1
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- Requires-Dist: pybind11
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- Requires-Dist: psutil
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- Requires-Dist: tifffile[all]
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- Requires-Dist: h5py
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-
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- # Python Template Matching Engine (PyTME)
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-
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- A software for template matching on electron microscopy data.
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-
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- 📖 **[Official Documentation](https://kosinskilab.github.io/pyTME/)** | 🚀 **[Installation Guide](https://kosinskilab.github.io/pyTME/quickstart/installation.html)** | 📚 **[API Reference](https://kosinskilab.github.io/pyTME/reference/index.html)**
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-
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- ### Installation
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-
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- There are three ways to get pyTME up and running:
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-
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- 1. **Install from Source:**
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- ```bash
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- pip install git+https://github.com/KosinskiLab/pyTME
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- ```
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-
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- 2. **Install from PyPi:**
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- ```bash
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- pip install pytme
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- ```
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-
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- 3. **Docker Container:**
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- Build and use the pyTME container from Docker. This assumes a linux/amd64 platform.
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- ```bash
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- docker build \
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- -t pytme \
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- --platform linux/amd64 \
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- -f docker/Dockerfile \
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- .
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- ```
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- 🔗 For more on the Docker container, visit the [Docker Hub page](https://hub.docker.com).
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-
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- ---
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-
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- ### Publication
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-
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- The pyTME publication is available on [SoftwareX](https://www.sciencedirect.com/science/article/pii/S2352711024000074).
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-
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- ```
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- @article{Maurer:2024aa,
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- author = {Maurer, Valentin J. and Siggel, Marc and Kosinski, Jan},
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- journal = {SoftwareX},
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- pages = {101636},
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- title = {PyTME (Python Template Matching Engine): A fast, flexible, and multi-purpose template matching library for cryogenic electron microscopy data},
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- volume = {25},
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- year = {2024}}
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- ```
@@ -1,66 +0,0 @@
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- scripts/extract_candidates.py,sha256=L2IXg99hgW8jUBp06e6PEDO-Y5iUhoFuhe0i5B9gcOE,6871
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- scripts/match_template.py,sha256=2p1-gF33N7JnLeE4QVFmQFVHG9HjliaDLyoFTYULjVM,26664
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- scripts/refine_matches.py,sha256=zV7piR5tGhrbomYN1tjnFDOfPInU07APU8syciSUZz8,7077
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- tme/__init__.py,sha256=MGVeRX1f5k6RwExBcffZtCM7igNNtpoIr2G2yJZ4OHI,251
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- tme/analyzer.py,sha256=qBasMmn4cnxWl3dEw-bkFQeyqtnLMuwgcmKuc0o2N5E,55632
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- tme/density.py,sha256=Tu37m-47ZWWs3wsR7G3dQmP69BNKZd3xdgmhBllR1EI,87856
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- tme/extensions.cpython-311-darwin.so,sha256=jUKGwYCpx9B6DAz3EDL5vPbfoxwQVM2KwQBizMDWkaA,412480
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- tme/helpers.py,sha256=TMtBuJoZk6q4M_rfkr8yPpGzJD74ycqyN3yXMuU9mr4,23625
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- tme/matching_constrained.py,sha256=NAJnZpusjQs5rKabHiNyrclXSPm27K0V8HVFjTQ2zB0,6725
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- tme/matching_data.py,sha256=OUyTVaELYCIqLExuf6Kps95Co4ymCHB0MypsaJOpmMA,24135
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- tme/matching_exhaustive.py,sha256=r45l45kMrjD3kTfKoZcVU3sl4C_1FOXfXGGWgUJu3_w,59531
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- tme/matching_memory.py,sha256=bmCAUYyXWEet-1XXhldtc0irio2ytMSsAzWYyFI5LNM,11273
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- tme/matching_optimization.py,sha256=oqZYk9hhquF9SmPiDZwSfxehirddxJUOIg3SbokgylI,41138
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- tme/matching_utils.py,sha256=b9aLcj4m0BmmJo4P8nivpd3rgic_WkounqLS3AJkB8g,42504
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- tme/orientations.py,sha256=sEGhwBIE19jeRsMr5OZ1VM5ccRBpN5uThx6xG9obbo0,19118
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- tme/parser.py,sha256=tA9ABeV95cZn8lJCukVUaocQ9RguR6ZZzQsMXf_-ud0,13887
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- tme/preprocessor.py,sha256=TFBmLA7ESfKF2cSbKB4PuDfjIxSyA6Hxccp1qpkDdQY,50760
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- tme/structure.py,sha256=1Dlh6gFn1VhoIr7H9ZDgOfaPJbVVfKv_c8AA00X_lbQ,52465
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- tme/types.py,sha256=2Tyh_xnMLxIWYb3aJDAUb6GWpaL6gcYMUm2YNbJlAPI,295
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- tme/backends/__init__.py,sha256=xB2GBUFRskppvEs6S74VH0Pi-nXnIvu9_QFhESlcl3Y,4366
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- tme/backends/cupy_backend.py,sha256=4x8vy3eIpHKmfjg5BtqB9J0-gP0fWcT85FY-rFRXgVU,13145
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- tme/backends/matching_backend.py,sha256=E3cMXnMEazYJUr9RP5Q5rMEAf3vbkiOwzWrx5amt_nI,29311
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- tme/backends/mlx_backend.py,sha256=MrwICZpUiAcpZXON70r4SH-KsWxfhq1PdHUe80WbT-k,8467
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- tme/backends/npfftw_backend.py,sha256=ZYUkcmUE_NXwvddfKrCorVPETjxbg0-5UJfjAMf3yc4,27451
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- tme/backends/pytorch_backend.py,sha256=0QrWX_MSE8ymhaniAzRBgMVL4h5QBJrbLbMbnnaWveE,18293
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- tme/data/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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- tme/data/c48n309.npy,sha256=NwH64mOEbm3tStq5c98o81fY1vMOoq4nvXDAh7Z7iZg,296768
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- tme/data/c48u1.npy,sha256=JeXMFzFITs2ezdc3x5lp3jo1cHHHHVADSA1Tpf77kXs,1088
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- tme/data/quat_to_numpy.py,sha256=-gkDZb10fKBxwfYrSLCUWvMB76TzZWELCeKsYProwws,1333
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