pytomography 2.0.0__tar.gz → 2.0.4__tar.gz

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Files changed (134) hide show
  1. {pytomography-2.0.0 → pytomography-2.0.4}/PKG-INFO +3 -2
  2. pytomography-2.0.4/docs/source/notebooks/t_PETGATE.ipynb +422 -0
  3. {pytomography-2.0.0 → pytomography-2.0.4}/docs/source/notebooks/t_dicomdata.ipynb +4 -4
  4. {pytomography-2.0.0 → pytomography-2.0.4}/docs/source/notebooks/t_dicommultibed.ipynb +13 -4
  5. pytomography-2.0.4/docs/source/notebooks/t_siminddata.ipynb +963 -0
  6. pytomography-2.0.4/docs/source/notebooks/t_uncertainty_spect.ipynb +457 -0
  7. {pytomography-2.0.0 → pytomography-2.0.4}/pyproject.toml +3 -2
  8. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/algorithms/__init__.py +1 -1
  9. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/algorithms/dip_recon.py +1 -0
  10. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/algorithms/preconditioned_gradient_ascent.py +237 -17
  11. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/callbacks/data_saving.py +1 -0
  12. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/callbacks/likelihood.py +2 -1
  13. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/io/PET/gate.py +31 -4
  14. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/io/SPECT/dicom.py +91 -45
  15. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/io/SPECT/shared.py +1 -1
  16. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/io/SPECT/simind.py +1 -1
  17. pytomography-2.0.4/src/pytomography/likelihoods/__init__.py +3 -0
  18. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/likelihoods/likelihood.py +14 -2
  19. pytomography-2.0.4/src/pytomography/likelihoods/mse_objective.py +67 -0
  20. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/likelihoods/poisson_log_likelihood.py +28 -2
  21. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/metadata/SPECT/spect_metadata.py +2 -0
  22. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/projectors/SPECT/spect_system_matrix.py +36 -21
  23. pytomography-2.0.4/src/pytomography/utils/scatter.py +7 -0
  24. pytomography-2.0.0/docs/source/notebooks/t_PETGATE.ipynb +0 -422
  25. pytomography-2.0.0/docs/source/notebooks/t_siminddata.ipynb +0 -954
  26. pytomography-2.0.0/docs/source/notebooks/t_uncertainty_spect.ipynb +0 -264
  27. pytomography-2.0.0/src/pytomography/likelihoods/__init__.py +0 -2
  28. pytomography-2.0.0/src/pytomography/utils/scatter.py +0 -2
  29. {pytomography-2.0.0 → pytomography-2.0.4}/.github/workflows/publish-to-test-pypi.yml +0 -0
  30. {pytomography-2.0.0 → pytomography-2.0.4}/.gitignore +0 -0
  31. {pytomography-2.0.0 → pytomography-2.0.4}/.readthedocs.yaml +0 -0
  32. {pytomography-2.0.0 → pytomography-2.0.4}/LICENSE +0 -0
  33. {pytomography-2.0.0 → pytomography-2.0.4}/README.md +0 -0
  34. {pytomography-2.0.0 → pytomography-2.0.4}/docs/Makefile +0 -0
  35. {pytomography-2.0.0 → pytomography-2.0.4}/docs/make.bat +0 -0
  36. {pytomography-2.0.0 → pytomography-2.0.4}/docs/source/_templates/autoapi/index.rst +0 -0
  37. {pytomography-2.0.0 → pytomography-2.0.4}/docs/source/_templates/autoapi/python/attribute.rst +0 -0
  38. {pytomography-2.0.0 → pytomography-2.0.4}/docs/source/_templates/autoapi/python/class.rst +0 -0
  39. {pytomography-2.0.0 → pytomography-2.0.4}/docs/source/_templates/autoapi/python/data.rst +0 -0
  40. {pytomography-2.0.0 → pytomography-2.0.4}/docs/source/_templates/autoapi/python/exception.rst +0 -0
  41. {pytomography-2.0.0 → pytomography-2.0.4}/docs/source/_templates/autoapi/python/function.rst +0 -0
  42. {pytomography-2.0.0 → pytomography-2.0.4}/docs/source/_templates/autoapi/python/method.rst +0 -0
  43. {pytomography-2.0.0 → pytomography-2.0.4}/docs/source/_templates/autoapi/python/module.rst +0 -0
  44. {pytomography-2.0.0 → pytomography-2.0.4}/docs/source/_templates/autoapi/python/package.rst +0 -0
  45. {pytomography-2.0.0 → pytomography-2.0.4}/docs/source/_templates/autoapi/python/property.rst +0 -0
  46. {pytomography-2.0.0 → pytomography-2.0.4}/docs/source/conf.py +0 -0
  47. {pytomography-2.0.0 → pytomography-2.0.4}/docs/source/developers_guide.md +0 -0
  48. {pytomography-2.0.0 → pytomography-2.0.4}/docs/source/external_data.md +0 -0
  49. {pytomography-2.0.0 → pytomography-2.0.4}/docs/source/images/PT1.png +0 -0
  50. {pytomography-2.0.0 → pytomography-2.0.4}/docs/source/images/coordinate_conventions.png +0 -0
  51. {pytomography-2.0.0 → pytomography-2.0.4}/docs/source/images/emission.png +0 -0
  52. {pytomography-2.0.0 → pytomography-2.0.4}/docs/source/images/figure4.jpg +0 -0
  53. {pytomography-2.0.0 → pytomography-2.0.4}/docs/source/images/figure5.jpg +0 -0
  54. {pytomography-2.0.0 → pytomography-2.0.4}/docs/source/images/psf.png +0 -0
  55. {pytomography-2.0.0 → pytomography-2.0.4}/docs/source/images/psf2.png +0 -0
  56. {pytomography-2.0.0 → pytomography-2.0.4}/docs/source/images/pytomo_front_title.png +0 -0
  57. {pytomography-2.0.0 → pytomography-2.0.4}/docs/source/images/sample_MIP.png +0 -0
  58. {pytomography-2.0.0 → pytomography-2.0.4}/docs/source/images/sample_MIPa.png +0 -0
  59. {pytomography-2.0.0 → pytomography-2.0.4}/docs/source/index.md +0 -0
  60. {pytomography-2.0.0 → pytomography-2.0.4}/docs/source/notebooks/conventions.ipynb +0 -0
  61. {pytomography-2.0.0 → pytomography-2.0.4}/docs/source/notebooks/script_to_generate_eta_for_petsird.py +0 -0
  62. {pytomography-2.0.0 → pytomography-2.0.4}/docs/source/notebooks/t_PETSIRD.ipynb +0 -0
  63. {pytomography-2.0.0 → pytomography-2.0.4}/docs/source/notebooks/t_fbp.ipynb +0 -0
  64. {pytomography-2.0.0 → pytomography-2.0.4}/docs/source/notebooks/t_quantitative.ipynb +0 -0
  65. {pytomography-2.0.0 → pytomography-2.0.4}/docs/source/usage.md +0 -0
  66. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/__init__.py +0 -0
  67. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/algorithms/fbp.py +0 -0
  68. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/callbacks/__init__.py +0 -0
  69. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/callbacks/callback.py +0 -0
  70. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/data/NIST_attenuation_data/adipose.csv +0 -0
  71. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/data/NIST_attenuation_data/air.csv +0 -0
  72. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/data/NIST_attenuation_data/aluminum.csv +0 -0
  73. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/data/NIST_attenuation_data/bonecortical.csv +0 -0
  74. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/data/NIST_attenuation_data/boneequivplastic.csv +0 -0
  75. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/data/NIST_attenuation_data/breast.csv +0 -0
  76. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/data/NIST_attenuation_data/lead.csv +0 -0
  77. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/data/NIST_attenuation_data/lungtissue.csv +0 -0
  78. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/data/NIST_attenuation_data/muscle.csv +0 -0
  79. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/data/NIST_attenuation_data/tissueequivplastic.csv +0 -0
  80. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/data/NIST_attenuation_data/tungsten.csv +0 -0
  81. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/data/NIST_attenuation_data/water.csv +0 -0
  82. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/data/collim.col +0 -0
  83. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/io/CT/__init__.py +0 -0
  84. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/io/CT/attenuation_map.py +0 -0
  85. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/io/PET/__init__.py +0 -0
  86. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/io/PET/petsird.py +0 -0
  87. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/io/PET/prd/__init__.py +0 -0
  88. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/io/PET/prd/_binary.py +0 -0
  89. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/io/PET/prd/_dtypes.py +0 -0
  90. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/io/PET/prd/_ndjson.py +0 -0
  91. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/io/PET/prd/binary.py +0 -0
  92. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/io/PET/prd/ndjson.py +0 -0
  93. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/io/PET/prd/protocols.py +0 -0
  94. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/io/PET/prd/types.py +0 -0
  95. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/io/PET/prd/yardl_types.py +0 -0
  96. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/io/SPECT/__init__.py +0 -0
  97. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/io/__init__.py +0 -0
  98. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/io/shared/__init__.py +0 -0
  99. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/io/shared/dicom.py +0 -0
  100. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/io/shared/dicom_creation.py +0 -0
  101. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/io/shared/interfile.py +0 -0
  102. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/metadata/PET/__init__.py +0 -0
  103. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/metadata/PET/pet_tof_metadata.py +0 -0
  104. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/metadata/PET/petlm_metadata.py +0 -0
  105. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/metadata/SPECT/__init__.py +0 -0
  106. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/metadata/__init__.py +0 -0
  107. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/metadata/metadata.py +0 -0
  108. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/priors/__init__.py +0 -0
  109. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/priors/nearest_neighbour.py +0 -0
  110. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/priors/prior.py +0 -0
  111. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/projectors/PET/__init__.py +0 -0
  112. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/projectors/PET/petlm_system_matrix.py +0 -0
  113. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/projectors/SPECT/__init__.py +0 -0
  114. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/projectors/__init__.py +0 -0
  115. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/projectors/shared/__init__.py +0 -0
  116. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/projectors/shared/kem_system_matrix.py +0 -0
  117. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/projectors/shared/motion_correction_system_matrix.py +0 -0
  118. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/projectors/system_matrix.py +0 -0
  119. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/transforms/SPECT/__init__.py +0 -0
  120. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/transforms/SPECT/attenuation.py +0 -0
  121. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/transforms/SPECT/cutoff.py +0 -0
  122. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/transforms/SPECT/psf.py +0 -0
  123. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/transforms/__init__.py +0 -0
  124. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/transforms/shared/__init__.py +0 -0
  125. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/transforms/shared/filters.py +0 -0
  126. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/transforms/shared/kem.py +0 -0
  127. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/transforms/shared/motion.py +0 -0
  128. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/transforms/shared/spatial.py +0 -0
  129. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/transforms/transform.py +0 -0
  130. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/utils/__init__.py +0 -0
  131. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/utils/fourier_filters.py +0 -0
  132. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/utils/misc.py +0 -0
  133. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/utils/nist_data.py +0 -0
  134. {pytomography-2.0.0 → pytomography-2.0.4}/src/pytomography/utils/spatial.py +0 -0
{pytomography-2.0.0 → pytomography-2.0.4}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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- Metadata-Version: 2.1
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+ Metadata-Version: 2.3
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  Name: pytomography
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- Version: 2.0.0
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+ Version: 2.0.4
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  Summary: Package to perform tomographic image reconstruction
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  Project-URL: Homepage, https://github.com/qurit/PyTomography
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  Project-URL: Bug Tracker, https://github.com/qurit/PyTomography/issues
@@ -13,6 +13,7 @@ Requires-Python: >=3.7
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  Requires-Dist: fft-conv-pytorch>=1.2.0
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  Requires-Dist: kornia>=0.6.12
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  Requires-Dist: matplotlib>=3.8.0
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+ Requires-Dist: nibabel>=5.1.0
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  Requires-Dist: numpy>=1.24.2
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  Requires-Dist: pydicom>=2.0.0
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  Requires-Dist: rt-utils>=1.2.0