pycistem 0.6.1__cp310-cp310-manylinux_2_28_x86_64.whl

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Files changed (84) hide show
  1. pycistem/__init__.py +9 -0
  2. pycistem/config.py +20 -0
  3. pycistem/core/__init__.py +1 -0
  4. pycistem/core/core.cpp +1070 -0
  5. pycistem/core/core.cpython-310-x86_64-linux-gnu.so +0 -0
  6. pycistem/core/database.cpp +408 -0
  7. pycistem/core/euler_search.cpp +72 -0
  8. pycistem/core/run_profiles.cpp +114 -0
  9. pycistem/database/__init__.py +301 -0
  10. pycistem/programs/__init__.py +10 -0
  11. pycistem/programs/_cistem_constants.py +23 -0
  12. pycistem/programs/apply_ctf.py +59 -0
  13. pycistem/programs/cistem_program.py +277 -0
  14. pycistem/programs/ctffind.py +254 -0
  15. pycistem/programs/estimate_beamtilt.py +60 -0
  16. pycistem/programs/match_template.py +325 -0
  17. pycistem/programs/reconstruct3d.py +79 -0
  18. pycistem/programs/refine_ctf.py +106 -0
  19. pycistem/programs/refine_template.py +157 -0
  20. pycistem/programs/refine_template_dev.py +35 -0
  21. pycistem/programs/refine_template_niko.py +124 -0
  22. pycistem/programs/resample.py +30 -0
  23. pycistem/programs/run_profile.py +17 -0
  24. pycistem/programs/unblur.py +247 -0
  25. pycistem/programs/unblur_patch.py +204 -0
  26. pycistem/utils/__init__.py +1 -0
  27. pycistem/utils/extract_particles.py +36 -0
  28. pycistem/utils/move_class_into_unbinned_particle_stack.py +34 -0
  29. pycistem/utils/order_by_class_occupancy.py +26 -0
  30. pycistem/utils/plot_class_occupancy.py +51 -0
  31. pycistem/utils/plot_classification_fsc_movie.py +90 -0
  32. pycistem/utils/plot_occupancy_by_condition.py +129 -0
  33. pycistem-0.6.1.dist-info/METADATA +258 -0
  34. pycistem-0.6.1.dist-info/RECORD +84 -0
  35. pycistem-0.6.1.dist-info/WHEEL +5 -0
  36. pycistem-0.6.1.dist-info/licenses/LICENSE +201 -0
  37. pycistem-0.6.1.dist-info/sboms/auditwheel.cdx.json +1 -0
  38. pycistem.libs/libXau-154567c4.so.6.0.0 +0 -0
  39. pycistem.libs/libXcomposite-9a78b2b5.so.1.0.0 +0 -0
  40. pycistem.libs/libXcursor-557eab0f.so.1.0.2 +0 -0
  41. pycistem.libs/libXdamage-45f20f14.so.1.1.0 +0 -0
  42. pycistem.libs/libXfixes-e3b7d94c.so.3.1.0 +0 -0
  43. pycistem.libs/libXi-9178a6bd.so.6.1.0 +0 -0
  44. pycistem.libs/libXinerama-6a3f4a3e.so.1.0.0 +0 -0
  45. pycistem.libs/libXrandr-9f75043e.so.2.2.0 +0 -0
  46. pycistem.libs/libatk-1-3e086f29.0.so.0.22810.1 +0 -0
  47. pycistem.libs/libblkid-a9167753.so.1.1.0 +0 -0
  48. pycistem.libs/libbz2-a1e77c99.so.1.0.6 +0 -0
  49. pycistem.libs/libcairo-dfbea965.so.2.11512.0 +0 -0
  50. pycistem.libs/libdatrie-584ecbbd.so.1.3.2 +0 -0
  51. pycistem.libs/libffi-3a37023a.so.6.0.2 +0 -0
  52. pycistem.libs/libfontconfig-dcb2ce6c.so.1.12.0 +0 -0
  53. pycistem.libs/libfreetype-2f3b32b6.so.6.16.1 +0 -0
  54. pycistem.libs/libfribidi-a2ddad26.so.0.4.0 +0 -0
  55. pycistem.libs/libgdk-x11-2-ae2f4865.0.so.0.2400.32 +0 -0
  56. pycistem.libs/libgdk_pixbuf-2-e875edac.0.so.0.3612.0 +0 -0
  57. pycistem.libs/libgio-2-54f4f0a9.0.so.0.5600.4 +0 -0
  58. pycistem.libs/libgmodule-2-a8eef785.0.so.0.5600.4 +0 -0
  59. pycistem.libs/libgmp-d944b113.so.10.3.2 +0 -0
  60. pycistem.libs/libgnutls-e5fc1c5f.so.30.28.2 +0 -0
  61. pycistem.libs/libgomp-e985bcbb.so.1.0.0 +0 -0
  62. pycistem.libs/libgraphite2-a2b39163.so.3.0.1 +0 -0
  63. pycistem.libs/libgtk-x11-2-76f42ab1.0.so.0.2400.32 +0 -0
  64. pycistem.libs/libharfbuzz-26b3d829.so.0.10705.0 +0 -0
  65. pycistem.libs/libhogweed-cd4c53be.so.4.5 +0 -0
  66. pycistem.libs/libidn2-2f4a5893.so.0.3.6 +0 -0
  67. pycistem.libs/libmount-ec61bd71.so.1.1.0 +0 -0
  68. pycistem.libs/libnettle-37944285.so.6.5 +0 -0
  69. pycistem.libs/libp11-kit-ac9dcd7e.so.0.3.0 +0 -0
  70. pycistem.libs/libpango-1-e80d1584.0.so.0.4200.3 +0 -0
  71. pycistem.libs/libpangocairo-1-e0e0fbcf.0.so.0.4200.3 +0 -0
  72. pycistem.libs/libpangoft2-1-1fa1613e.0.so.0.4200.3 +0 -0
  73. pycistem.libs/libpcre-0dd207b5.so.1.2.10 +0 -0
  74. pycistem.libs/libpcre2-8-516f4c9d.so.0.7.1 +0 -0
  75. pycistem.libs/libpixman-1-06469c37.so.0.38.4 +0 -0
  76. pycistem.libs/libpng16-748299c7.so.16.34.0 +0 -0
  77. pycistem.libs/libselinux-d0805dcb.so.1 +0 -0
  78. pycistem.libs/libtasn1-564de53e.so.6.5.5 +0 -0
  79. pycistem.libs/libthai-cd935638.so.0.3.0 +0 -0
  80. pycistem.libs/libunistring-05abdd40.so.2.1.0 +0 -0
  81. pycistem.libs/libuuid-95b83d40.so.1.3.0 +0 -0
  82. pycistem.libs/libxcb-5ddf6756.so.1.1.0 +0 -0
  83. pycistem.libs/libxcb-render-161c0eb5.so.0.0.0 +0 -0
  84. pycistem.libs/libxcb-shm-0be6dfbf.so.0.0.0 +0 -0
pycistem/__init__.py ADDED
@@ -0,0 +1,9 @@
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+ __version__ = "0.6.1"
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+
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+ #from . import core
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+ from pycistem import database, programs, utils
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+ from pycistem.config import set_cistem_path
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+
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+
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+
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+
pycistem/config.py ADDED
@@ -0,0 +1,20 @@
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+ from pathlib import Path
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+
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+ import appdirs
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+ import yaml
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+
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+ config = {
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+ "CISTEM_PATH": "/usr/local/bin/"
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+ }
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+ config_path = Path(appdirs.user_config_dir("pycistem","cistem")) / "config.yaml"
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+ if config_path.exists():
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+ with open(config_path) as fp:
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+ config_file = yaml.safe_load(fp)
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+ if "CISTEM_PATH" in config:
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+ config["CISTEM_PATH"] = config_file["CISTEM_PATH"]
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+
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+ def set_cistem_path(path):
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+ config["CISTEM_PATH"] = path
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+ config_path.parent.mkdir(parents=True,exist_ok=True)
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+ with open(config_path,"w") as fp:
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+ yaml.dump(config,fp)
pycistem/core/__init__.py ADDED
@@ -0,0 +1 @@
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+ from pycistem.core.core import *