nabu 2024.1.1__py3-none-any.whl → 2024.1.2__py3-none-any.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 (2095) hide show
  1. nabu/__init__.py +1 -1
  2. nabu/app/cast_volume.py +11 -2
  3. nabu/app/multicor.py +24 -2
  4. nabu/io/cast_volume.py +3 -3
  5. nabu/io/utils.py +2 -2
  6. nabu/stitching/tests/test_z_stitching.py +0 -1
  7. nabu/stitching/z_stitching.py +3 -3
  8. {nabu-2024.1.1.dist-info → nabu-2024.1.2.dist-info}/METADATA +2 -2
  9. nabu-2024.1.2.dist-info/RECORD +296 -0
  10. {nabu-2024.1.1.dist-info → nabu-2024.1.2.dist-info}/WHEEL +1 -1
  11. nabu-2024.1.2.dist-info/top_level.txt +2 -0
  12. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/doc/conf.py +0 -137
  13. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/doc/create_conf_doc.py +0 -38
  14. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/doc/get_mathjax.py +0 -34
  15. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/__init__.py +0 -17
  16. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/bootstrap.py +0 -88
  17. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/bootstrap_stitching.py +0 -69
  18. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/cast_volume.py +0 -272
  19. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/cli_configs.py +0 -626
  20. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/compare_volumes.py +0 -94
  21. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/composite_cor.py +0 -144
  22. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/correct_rot.py +0 -70
  23. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/create_distortion_map_from_poly.py +0 -153
  24. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/diag_to_pix.py +0 -358
  25. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/diag_to_rot.py +0 -449
  26. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/double_flatfield.py +0 -143
  27. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/generate_header.py +0 -261
  28. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/histogram.py +0 -197
  29. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/multicor.py +0 -90
  30. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/nx_z_splitter.py +0 -125
  31. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/parse_reconstruction_log.py +0 -151
  32. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/prepare_weights_double.py +0 -163
  33. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/reconstruct.py +0 -120
  34. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/reconstruct_helical.py +0 -116
  35. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/reduce_dark_flat.py +0 -181
  36. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/rotate.py +0 -162
  37. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/shrink_dataset.py +0 -98
  38. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/stitching.py +0 -85
  39. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/tests/test_reduce_dark_flat.py +0 -78
  40. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/utils.py +0 -33
  41. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/validator.py +0 -110
  42. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/__init__.py +0 -0
  43. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/convolution.py +0 -8
  44. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/fft.py +0 -4
  45. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/kernel.py +0 -97
  46. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/medfilt.py +0 -6
  47. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/padding.py +0 -6
  48. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/processing.py +0 -75
  49. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/tests/__init__.py +0 -1
  50. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/utils.py +0 -331
  51. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/__init__.py +0 -12
  52. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/alignment.py +0 -578
  53. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/cor.py +0 -1621
  54. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/cor_sino.py +0 -183
  55. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/distortion.py +0 -112
  56. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/focus.py +0 -362
  57. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/__init__.py +0 -0
  58. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_alignment.py +0 -70
  59. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_cor.py +0 -472
  60. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_focus.py +0 -105
  61. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_tilt.py +0 -41
  62. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_translation.py +0 -78
  63. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tilt.py +0 -214
  64. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/translation.py +0 -193
  65. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/utils.py +0 -39
  66. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/__init__.py +0 -2
  67. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/cast_volume.py +0 -371
  68. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/detector_distortion.py +0 -305
  69. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/reader.py +0 -628
  70. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/reader_helical.py +0 -114
  71. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tests/__init__.py +0 -0
  72. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tests/test_cast_volume.py +0 -339
  73. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tests/test_detector_distortion.py +0 -178
  74. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tests/test_writers.py +0 -187
  75. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tiffwriter_zmm.py +0 -99
  76. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/utils.py +0 -263
  77. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/writer.py +0 -892
  78. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/__init__.py +0 -0
  79. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/binning.py +0 -98
  80. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/fftshift.py +0 -6
  81. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/filters.py +0 -24
  82. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/fourier_filters.py +0 -152
  83. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/histogram.py +0 -6
  84. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/histogram_cuda.py +0 -8
  85. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/kernel_base.py +0 -4
  86. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/padding.py +0 -83
  87. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/padding_base.py +0 -6
  88. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/processing_base.py +0 -4
  89. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/rotation.py +0 -6
  90. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/rotation_cuda.py +0 -6
  91. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/tests/__init__.py +0 -1
  92. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/tests/test_binning.py +0 -48
  93. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/tests/test_interpolation.py +0 -70
  94. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/transpose.py +0 -6
  95. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/unsharp.py +0 -4
  96. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/unsharp_cuda.py +0 -6
  97. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/unsharp_opencl.py +0 -8
  98. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/utils.py +0 -117
  99. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/__init__.py +0 -0
  100. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/fft.py +0 -6
  101. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/kernel.py +0 -135
  102. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/memcpy.py +0 -35
  103. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/padding.py +0 -6
  104. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/processing.py +0 -62
  105. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/tests/__init__.py +0 -0
  106. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/utils.py +0 -292
  107. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/__init__.py +0 -0
  108. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/config.py +0 -265
  109. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/config_validators.py +0 -589
  110. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/datadump.py +0 -164
  111. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/dataset_validator.py +0 -211
  112. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/detector_distortion_provider.py +0 -20
  113. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/estimators.py +0 -1012
  114. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fallback_utils.py +0 -149
  115. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/__init__.py +0 -0
  116. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/chunked.py +0 -849
  117. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/chunked_cuda.py +0 -152
  118. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/computations.py +0 -260
  119. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/dataset_validator.py +0 -63
  120. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/nabu_config.py +0 -590
  121. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/processconfig.py +0 -825
  122. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/reconstruction.py +0 -851
  123. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/__init__.py +0 -0
  124. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/dataset_validator.py +0 -19
  125. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/fbp.py +0 -147
  126. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/filtering.py +0 -246
  127. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/gridded_accumulator.py +0 -575
  128. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_chunked_regridded.py +0 -1670
  129. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_chunked_regridded_cuda.py +0 -119
  130. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_reconstruction.py +0 -598
  131. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_utils.py +0 -42
  132. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/nabu_config.py +0 -175
  133. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/processconfig.py +0 -62
  134. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/span_strategy.py +0 -483
  135. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/__init__.py +0 -0
  136. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/test_accumulator.py +0 -157
  137. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/test_pipeline_elements_full.py +0 -355
  138. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/test_strategy.py +0 -61
  139. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/utils.py +0 -51
  140. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/weight_balancer.py +0 -101
  141. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/params.py +0 -163
  142. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/processconfig.py +0 -210
  143. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/tests/test_chunk_reader.py +0 -78
  144. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/tests/test_estimators.py +0 -149
  145. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/utils.py +0 -116
  146. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/writer.py +0 -193
  147. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/xrdct/__init__.py +0 -0
  148. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/__init__.py +0 -7
  149. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/alignment.py +0 -11
  150. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ccd.py +0 -161
  151. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ccd_cuda.py +0 -169
  152. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ctf.py +0 -361
  153. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ctf_cuda.py +0 -142
  154. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/distortion.py +0 -92
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  1979. build/lib/nabu/preproc/flatfield_cuda.py +0 -144
  1980. build/lib/nabu/preproc/flatfield_variable_region.py +0 -79
  1981. build/lib/nabu/preproc/phase.py +0 -425
  1982. build/lib/nabu/preproc/phase_cuda.py +0 -143
  1983. build/lib/nabu/preproc/shift.py +0 -95
  1984. build/lib/nabu/preproc/shift_cuda.py +0 -102
  1985. build/lib/nabu/preproc/tests/__init__.py +0 -1
  1986. build/lib/nabu/preproc/tests/test_ccd_corr.py +0 -59
  1987. build/lib/nabu/preproc/tests/test_ctf.py +0 -250
  1988. build/lib/nabu/preproc/tests/test_double_flatfield.py +0 -86
  1989. build/lib/nabu/preproc/tests/test_flatfield.py +0 -626
  1990. build/lib/nabu/preproc/tests/test_paganin.py +0 -67
  1991. build/lib/nabu/preproc/tests/test_vshift.py +0 -73
  1992. build/lib/nabu/processing/__init__.py +0 -0
  1993. build/lib/nabu/processing/convolution_cuda.py +0 -375
  1994. build/lib/nabu/processing/fft_base.py +0 -163
  1995. build/lib/nabu/processing/fft_cuda.py +0 -256
  1996. build/lib/nabu/processing/fft_opencl.py +0 -54
  1997. build/lib/nabu/processing/fftshift.py +0 -134
  1998. build/lib/nabu/processing/histogram.py +0 -286
  1999. build/lib/nabu/processing/histogram_cuda.py +0 -103
  2000. build/lib/nabu/processing/kernel_base.py +0 -126
  2001. build/lib/nabu/processing/medfilt_cuda.py +0 -159
  2002. build/lib/nabu/processing/muladd.py +0 -29
  2003. build/lib/nabu/processing/muladd_cuda.py +0 -68
  2004. build/lib/nabu/processing/padding_base.py +0 -71
  2005. build/lib/nabu/processing/padding_cuda.py +0 -75
  2006. build/lib/nabu/processing/padding_opencl.py +0 -77
  2007. build/lib/nabu/processing/processing_base.py +0 -123
  2008. build/lib/nabu/processing/roll_opencl.py +0 -64
  2009. build/lib/nabu/processing/rotation.py +0 -63
  2010. build/lib/nabu/processing/rotation_cuda.py +0 -66
  2011. build/lib/nabu/processing/tests/__init__.py +0 -0
  2012. build/lib/nabu/processing/tests/test_fft.py +0 -268
  2013. build/lib/nabu/processing/tests/test_fftshift.py +0 -71
  2014. build/lib/nabu/processing/tests/test_histogram.py +0 -55
  2015. build/lib/nabu/processing/tests/test_medfilt.py +0 -77
  2016. build/lib/nabu/processing/tests/test_muladd.py +0 -54
  2017. build/lib/nabu/processing/tests/test_padding.py +0 -247
  2018. build/lib/nabu/processing/tests/test_roll.py +0 -63
  2019. build/lib/nabu/processing/tests/test_rotation.py +0 -83
  2020. build/lib/nabu/processing/tests/test_transpose.py +0 -72
  2021. build/lib/nabu/processing/tests/test_unsharp.py +0 -106
  2022. build/lib/nabu/processing/transpose.py +0 -126
  2023. build/lib/nabu/processing/unsharp.py +0 -79
  2024. build/lib/nabu/processing/unsharp_cuda.py +0 -53
  2025. build/lib/nabu/processing/unsharp_opencl.py +0 -75
  2026. build/lib/nabu/reconstruction/__init__.py +0 -3
  2027. build/lib/nabu/reconstruction/cone.py +0 -241
  2028. build/lib/nabu/reconstruction/fbp.py +0 -124
  2029. build/lib/nabu/reconstruction/fbp_base.py +0 -391
  2030. build/lib/nabu/reconstruction/fbp_opencl.py +0 -78
  2031. build/lib/nabu/reconstruction/filtering.py +0 -220
  2032. build/lib/nabu/reconstruction/filtering_cuda.py +0 -103
  2033. build/lib/nabu/reconstruction/filtering_opencl.py +0 -111
  2034. build/lib/nabu/reconstruction/projection.py +0 -240
  2035. build/lib/nabu/reconstruction/reconstructor.py +0 -174
  2036. build/lib/nabu/reconstruction/reconstructor_cuda.py +0 -44
  2037. build/lib/nabu/reconstruction/rings.py +0 -248
  2038. build/lib/nabu/reconstruction/rings_cuda.py +0 -322
  2039. build/lib/nabu/reconstruction/sinogram.py +0 -467
  2040. build/lib/nabu/reconstruction/sinogram_cuda.py +0 -250
  2041. build/lib/nabu/reconstruction/sinogram_opencl.py +0 -40
  2042. build/lib/nabu/reconstruction/tests/__init__.py +0 -1
  2043. build/lib/nabu/reconstruction/tests/test_cone.py +0 -308
  2044. build/lib/nabu/reconstruction/tests/test_deringer.py +0 -220
  2045. build/lib/nabu/reconstruction/tests/test_fbp.py +0 -252
  2046. build/lib/nabu/reconstruction/tests/test_filtering.py +0 -133
  2047. build/lib/nabu/reconstruction/tests/test_halftomo.py +0 -100
  2048. build/lib/nabu/reconstruction/tests/test_projector.py +0 -164
  2049. build/lib/nabu/reconstruction/tests/test_reconstructor.py +0 -93
  2050. build/lib/nabu/reconstruction/tests/test_sino_normalization.py +0 -85
  2051. build/lib/nabu/resources/__init__.py +0 -0
  2052. build/lib/nabu/resources/cli/__init__.py +0 -0
  2053. build/lib/nabu/resources/cor.py +0 -5
  2054. build/lib/nabu/resources/dataset_analyzer.py +0 -469
  2055. build/lib/nabu/resources/gpu.py +0 -169
  2056. build/lib/nabu/resources/logger.py +0 -130
  2057. build/lib/nabu/resources/nxflatfield.py +0 -217
  2058. build/lib/nabu/resources/templates/__init__.py +0 -0
  2059. build/lib/nabu/resources/tests/__init__.py +0 -0
  2060. build/lib/nabu/resources/tests/test_nxflatfield.py +0 -104
  2061. build/lib/nabu/resources/tests/test_units.py +0 -47
  2062. build/lib/nabu/resources/utils.py +0 -174
  2063. build/lib/nabu/stitching/__init__.py +0 -0
  2064. build/lib/nabu/stitching/alignment.py +0 -184
  2065. build/lib/nabu/stitching/config.py +0 -1286
  2066. build/lib/nabu/stitching/definitions.py +0 -6
  2067. build/lib/nabu/stitching/frame_composition.py +0 -155
  2068. build/lib/nabu/stitching/overlap.py +0 -373
  2069. build/lib/nabu/stitching/sample_normalization.py +0 -60
  2070. build/lib/nabu/stitching/slurm_utils.py +0 -204
  2071. build/lib/nabu/stitching/tests/__init__.py +0 -0
  2072. build/lib/nabu/stitching/tests/test_alignment.py +0 -99
  2073. build/lib/nabu/stitching/tests/test_config.py +0 -226
  2074. build/lib/nabu/stitching/tests/test_frame_composition.py +0 -180
  2075. build/lib/nabu/stitching/tests/test_overlap.py +0 -98
  2076. build/lib/nabu/stitching/tests/test_sample_normalization.py +0 -49
  2077. build/lib/nabu/stitching/tests/test_slurm_utils.py +0 -146
  2078. build/lib/nabu/stitching/tests/test_utils.py +0 -21
  2079. build/lib/nabu/stitching/tests/test_z_stitching.py +0 -1183
  2080. build/lib/nabu/stitching/utils.py +0 -563
  2081. build/lib/nabu/stitching/z_stitching.py +0 -2279
  2082. build/lib/nabu/tests.py +0 -51
  2083. build/lib/nabu/testutils.py +0 -375
  2084. build/lib/nabu/thirdparty/__init__.py +0 -0
  2085. build/lib/nabu/thirdparty/algotom_convert_sino.py +0 -276
  2086. build/lib/nabu/thirdparty/pore3d_deringer_munch.py +0 -108
  2087. build/lib/nabu/thirdparty/tomocupy_remove_stripe.py +0 -586
  2088. build/lib/nabu/thirdparty/tomopy_phase.py +0 -239
  2089. build/lib/nabu/thirdparty/tomwer_load_flats_darks.py +0 -162
  2090. build/lib/nabu/utils.py +0 -836
  2091. nabu-2024.1.1.dist-info/RECORD +0 -2375
  2092. nabu-2024.1.1.dist-info/top_level.txt +0 -4
  2093. {build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app → nabu/app/tests}/__init__.py +0 -0
  2094. {nabu-2024.1.1.dist-info → nabu-2024.1.2.dist-info}/LICENSE +0 -0
  2095. {nabu-2024.1.1.dist-info → nabu-2024.1.2.dist-info}/entry_points.txt +0 -0
@@ -1,425 +0,0 @@
1
- from math import pi
2
- from bisect import bisect
3
- import numpy as np
4
- from scipy.fft import rfft2, irfft2, fft2, ifft2
5
- from ..utils import generate_powers, get_decay, check_supported, get_num_threads, deprecation_warning
6
-
7
- #
8
- from .ctf import CTFPhaseRetrieval
9
-
10
- #
11
-
12
-
13
- def lmicron_to_db(Lmicron, energy, distance):
14
- """
15
- Utility to convert the "Lmicron" parameter of PyHST
16
- to a value of delta/beta.
17
-
18
- Parameters
19
- -----------
20
- Lmicron: float
21
- Length in microns, values of the parameter "PAGANIN_Lmicron"
22
- in PyHST2 parameter file.
23
- energy: float
24
- Energy in keV.
25
- distance: float
26
- Sample-detector distance in microns
27
-
28
- Notes
29
- --------
30
- The conversion is done using the formula
31
-
32
- .. math::
33
- L^2 = \\pi \\lambda D \\frac{\\delta}{\\beta}
34
-
35
- """
36
- L2 = Lmicron**2
37
- wavelength = 1.23984199e-3 / energy
38
- return L2 / (pi * wavelength * distance)
39
-
40
-
41
- class PaganinPhaseRetrieval:
42
- available_padding_modes = ["zeros", "mean", "edge", "symmetric", "reflect"]
43
- powers = generate_powers()
44
-
45
- def __init__(
46
- self,
47
- shape,
48
- distance=0.5,
49
- energy=20,
50
- delta_beta=250.0,
51
- pixel_size=1e-6,
52
- padding="edge",
53
- margin=None,
54
- use_rfft=True,
55
- use_R2C=None,
56
- fftw_num_threads=None,
57
- fft_num_threads=None,
58
- ):
59
- """
60
- Paganin Phase Retrieval for an infinitely distant point source.
61
- Formula (10) in [1].
62
-
63
- Parameters
64
- ----------
65
- shape: int or tuple
66
- Shape of each radio, in the format (num_rows, num_columns), i.e
67
- (size_vertical, size_horizontal).
68
- If an integer is provided, the shape is assumed to be square.
69
- distance : float, optional
70
- Propagation distance in meters.
71
- energy : float, optional
72
- Energy in keV.
73
- delta_beta: float, optional
74
- delta/beta ratio, where n = (1 - delta) + i*beta is the complex
75
- refractive index of the sample.
76
- pixel_size : float, optional
77
- Detector pixel size in meters. Default is 1e-6 (one micron)
78
- padding : str, optional
79
- Padding method. Available are "zeros", "mean", "edge", "sym",
80
- "reflect". Default is "edge".
81
- Please refer to the "Padding" section below for more details.
82
- margin: tuple, optional
83
- The user may provide integers values U, D, L, R as a tuple under the
84
- form ((U, D), (L, R)) (same syntax as numpy.pad()).
85
- The resulting filtered radio will have a size equal to
86
- (size_vertic - U - D, size_horiz - L - R).
87
- These values serve to create a "margin" for the filtering process,
88
- where U, D, L R are the margin of the Up, Down, Left and Right part,
89
- respectively.
90
- The filtering is done on a subset of the input radio. The subset
91
- size is (Nrows - U - D, Ncols - R - L).
92
- The margins is used to do the padding for the rest of the padded
93
- array.
94
-
95
- For example in one dimension, where ``padding="edge"``::
96
-
97
- <------------------------------ padded_size --------------------------->
98
- [padding=edge | padding=data | radio data | padding=data | padding=edge]
99
- <------ N2 ---><----- L -----><- (N-L-R)--><----- R -----><----- N2 --->
100
-
101
- Some or all the values U, D, L, R can be 0. In this case,
102
- the padding of the parts related to the zero values will
103
- fall back to the one of "padding" parameter.
104
- For example, if padding="edge" and L, R are 0, then
105
- the left and right parts will be padded with the edges, while
106
- the Up and Down parts will be padded using the the user-provided
107
- margins of the radio, and the final data will have shape
108
- (Nrows - U - D, Ncols).
109
- Some or all the values U, D, L, R can be the string "auto".
110
- In this case, the values of U, D, L, R are automatically computed
111
- as a function of the Paganin filter width.
112
- use_rfft: bool, optional
113
- Whether to use Real-to-Complex (R2C) transform instead of
114
- standard Complex-to-Complex transform, providing better performances
115
- use_R2C: bool, optional
116
- DEPRECATED, use use_rfft instead
117
- fftw_num_threads: bool or None or int, optional
118
- DEPRECATED - please use fft_num_threads
119
- fft_num_threads: bool or None or int, optional
120
- Number of threads for FFT.
121
- Default is to use all available threads. You can pass a negative number
122
- to use N - fft_num_threads cores.
123
-
124
- Important
125
- ----------
126
- Mind the units! Distance and pixel size are in meters, and energy is in keV.
127
-
128
-
129
- Notes
130
- ------
131
-
132
- **Padding methods**
133
-
134
- The phase retrieval is a convolution done in Fourier domain using FFT,
135
- so the Fourier transform size has to be at least twice the size of
136
- the original data. Mathematically, the data should be padded with zeros
137
- before being Fourier transformed. However, in practice, this can lead
138
- to artefacts at the edges (Gibbs effect) if the data does not go to
139
- zero at the edges.
140
- Apart from applying an apodization (Hamming, Blackman, etc), a common
141
- strategy to avoid these artefacts is to pad the data.
142
- In tomography reconstruction, this is usually done by replicating the
143
- last(s) value(s) of the edges ; but one can think of other methods:
144
-
145
- - "zeros": the data is simply padded with zeros.
146
- - "mean": the upper side of extended data is padded with the mean of
147
- the first row, the lower side with the mean of the last row, etc.
148
- - "edge": the data is padded by replicating the edges.
149
- This is the default mode.
150
- - "sym": the data is padded by mirroring the data with respect
151
- to its edges. See ``numpy.pad()``.
152
- - "reflect": the data is padded by reflecting the data with respect
153
- to its edges, including the edges. See ``numpy.pad()``.
154
-
155
-
156
- **Formulas**
157
-
158
- The radio is divided, in the Fourier domain, by the original "Paganin filter" `[1]`.
159
-
160
- .. math::
161
-
162
- F = 1 + \\frac{\\delta}{\\beta} \\lambda D \\pi |k|^2
163
-
164
- where k is the wave vector.
165
-
166
-
167
- References
168
- -----------
169
- [1] D. Paganin Et Al, "Simultaneous phase and amplitude extraction
170
- from a single defocused image of a homogeneous object",
171
- Journal of Microscopy, Vol 206, Part 1, 2002
172
- """
173
- self._init_parameters(distance, energy, pixel_size, delta_beta, padding)
174
- self._calc_shape(shape, margin)
175
- # COMPAT.
176
- if use_R2C is not None:
177
- deprecation_warning("'use_R2C' is replaced with 'use_rfft'", func_name="pag_r2c")
178
- if fftw_num_threads is not None:
179
- deprecation_warning("'fftw_num_threads' is replaced with 'fft_num_threads'", func_name="pag_fftw")
180
- fft_num_threads = fftw_num_threads
181
- # ---
182
- self._get_fft(use_rfft, fft_num_threads)
183
- self.compute_filter()
184
-
185
- def _init_parameters(self, distance, energy, pixel_size, delta_beta, padding):
186
- self.distance_cm = distance * 1e2
187
- self.distance_micron = distance * 1e6
188
- self.energy_kev = energy
189
- self.pixel_size_micron = pixel_size * 1e6
190
- self.delta_beta = delta_beta
191
- self.wavelength_micron = 1.23984199e-3 / self.energy_kev
192
- self.padding = padding
193
- self.padding_methods = {
194
- "zeros": self._pad_zeros,
195
- "mean": self._pad_mean,
196
- "edge": self._pad_edge,
197
- "symmetric": self._pad_sym,
198
- "reflect": self._pad_reflect,
199
- }
200
-
201
- def _get_fft(self, use_rfft, fft_num_threads):
202
- self.use_rfft = use_rfft
203
- self.use_R2C = use_rfft # Compat.
204
- self.fft_num_threads = get_num_threads(fft_num_threads)
205
- if self.use_rfft:
206
- self.fft_func = rfft2
207
- self.ifft_func = irfft2
208
- else:
209
- self.fft_func = fft2
210
- self.ifft_func = ifft2
211
-
212
- def _calc_shape(self, shape, margin):
213
- if np.isscalar(shape):
214
- shape = (shape, shape)
215
- else:
216
- assert len(shape) == 2
217
- self.shape = shape
218
- self._set_margin_value(margin)
219
- self._calc_padded_shape()
220
-
221
- def _set_margin_value(self, margin):
222
- self.margin = margin
223
- if margin is None:
224
- self.shape_inner = self.shape
225
- self.use_margin = False
226
- self.margin = ((0, 0), (0, 0))
227
- return
228
- self.use_margin = True
229
- try:
230
- ((U, D), (L, R)) = margin
231
- except ValueError:
232
- raise ValueError("Expected margin in the format ((U, D), (L, R))")
233
- for val in [U, D, L, R]:
234
- if isinstance(val, str) and val != "auto":
235
- raise ValueError("Expected either an integer, or 'auto'")
236
- if int(val) != val or val < 0:
237
- raise ValueError("Expected positive integers for margin values")
238
- self.shape_inner = (self.shape[0] - U - D, self.shape[1] - L - R)
239
-
240
- def _calc_padded_shape(self):
241
- """
242
- Compute the padded shape.
243
- If margin = 0, length_padded = next_power(2*length).
244
- Otherwise : length_padded = next_power(2*(length - margins))
245
-
246
- Principle
247
- ----------
248
-
249
- <--------------------- nx_p --------------------->
250
- | | original data | |
251
- < -- Pl - ><-- L -->< -- nx --><-- R --><-- Pr -->
252
- <----------- nx0 ----------->
253
-
254
- Pl, Pr : left/right padding length
255
- L, R : left/right margin
256
- nx : length of inner data (and length of final result)
257
- nx0 : length of original data
258
- nx_p : total length of padded data
259
- """
260
- n_y, n_x = self.shape_inner
261
- n_y0, n_x0 = self.shape
262
- n_y_p = self._get_next_power(max(2 * n_y, n_y0))
263
- n_x_p = self._get_next_power(max(2 * n_x, n_x0))
264
- self.shape_padded = (n_y_p, n_x_p)
265
- self.data_padded = np.zeros((n_y_p, n_x_p), dtype=np.float64)
266
-
267
- ((U, D), (L, R)) = self.margin
268
- n_y0, n_x0 = self.shape
269
- self.pad_top_len = (n_y_p - n_y0) // 2
270
- self.pad_bottom_len = n_y_p - n_y0 - self.pad_top_len
271
- self.pad_left_len = (n_x_p - n_x0) // 2
272
- self.pad_right_len = n_x_p - n_x0 - self.pad_left_len
273
-
274
- def _get_next_power(self, n):
275
- """
276
- Given a number, get the closest (upper) number p such that
277
- p is a power of 2, 3, 5 and 7.
278
- """
279
- idx = bisect(self.powers, n)
280
- if self.powers[idx - 1] == n:
281
- return n
282
- return self.powers[idx]
283
-
284
- def compute_filter(self):
285
- nyp, nxp = self.shape_padded
286
- fftfreq = np.fft.rfftfreq if self.use_rfft else np.fft.fftfreq
287
- fy = np.fft.fftfreq(nyp, d=self.pixel_size_micron)
288
- fx = fftfreq(nxp, d=self.pixel_size_micron)
289
- self._coords_grid = np.add.outer(fy**2, fx**2)
290
- #
291
- k2 = self._coords_grid
292
- D = self.distance_micron
293
- L = self.wavelength_micron
294
- db = self.delta_beta
295
- self.paganin_filter = 1.0 / (1 + db * L * D * pi * k2)
296
-
297
- def pad_with_values(self, data, top_val=0, bottom_val=0, left_val=0, right_val=0):
298
- """
299
- Pad the data into `self.padded_data` with values.
300
-
301
- Parameters
302
- ----------
303
- data: numpy.ndarray
304
- data (radio)
305
- top_val: float or numpy.ndarray, optional
306
- Value(s) to fill the top of the padded data with.
307
- bottom_val: float or numpy.ndarray, optional
308
- Value(s) to fill the bottom of the padded data with.
309
- left_val: float or numpy.ndarray, optional
310
- Value(s) to fill the left of the padded data with.
311
- right_val: float or numpy.ndarray, optional
312
- Value(s) to fill the right of the padded data with.
313
- """
314
- self.data_padded.fill(0)
315
- Pu, Pd = self.pad_top_len, self.pad_bottom_len
316
- Pl, Pr = self.pad_left_len, self.pad_right_len
317
- self.data_padded[:Pu, :] = top_val
318
- self.data_padded[-Pd:, :] = bottom_val
319
- self.data_padded[:, :Pl] = left_val
320
- self.data_padded[:, -Pr:] = right_val
321
- self.data_padded[Pu:-Pd, Pl:-Pr] = data
322
- # Transform the data to the FFT layout
323
- self.data_padded = np.roll(self.data_padded, (-Pu, -Pl), axis=(0, 1))
324
-
325
- def _pad_zeros(self, data):
326
- return self.pad_with_values(data, top_val=0, bottom_val=0, left_val=0, right_val=0)
327
-
328
- def _pad_mean(self, data):
329
- """
330
- Pad the data at each border with a different constant value.
331
- The value depends on the padding size:
332
- - On the left, value = mean(first data column)
333
- - On the right, value = mean(last data column)
334
- - On the top, value = mean(first data row)
335
- - On the bottom, value = mean(last data row)
336
- """
337
- return self.pad_with_values(
338
- data,
339
- top_val=np.mean(data[0, :]),
340
- bottom_val=np.mean(data[-1, :]),
341
- left_val=np.mean(data[:, 0]),
342
- right_val=np.mean(data[:, -1]),
343
- )
344
-
345
- def _pad_numpy(self, data, mode):
346
- data_padded = np.pad(
347
- data, ((self.pad_top_len, self.pad_bottom_len), (self.pad_left_len, self.pad_right_len)), mode=mode
348
- )
349
- # Transform the data to the FFT layout
350
- Pu, Pl = self.pad_top_len, self.pad_left_len
351
- return np.roll(data_padded, (-Pu, -Pl), axis=(0, 1))
352
-
353
- def _pad_edge(self, data):
354
- self.data_padded = self._pad_numpy(data, mode="edge")
355
-
356
- def _pad_sym(self, data):
357
- self.data_padded = self._pad_numpy(data, mode="symmetric")
358
-
359
- def _pad_reflect(self, data):
360
- self.data_padded = self._pad_numpy(data, mode="reflect")
361
-
362
- def pad_data(self, data, padding_method=None):
363
- padding_method = padding_method or self.padding
364
- check_supported(padding_method, self.available_padding_modes, "padding mode")
365
- if padding_method not in self.padding_methods:
366
- raise ValueError(
367
- "Unknown padding method %s. Available are: %s"
368
- % (padding_method, str(list(self.padding_methods.keys())))
369
- )
370
- pad_func = self.padding_methods[padding_method]
371
- pad_func(data)
372
- return self.data_padded
373
-
374
- def apply_filter(self, radio, padding_method=None, output=None):
375
- self.pad_data(radio, padding_method=padding_method)
376
- radio_f = self.fft_func(self.data_padded, workers=self.fft_num_threads)
377
- radio_f *= self.paganin_filter
378
- radio_filtered = self.ifft_func(radio_f, workers=self.fft_num_threads).real
379
- s0, s1 = self.shape_inner
380
- ((U, _), (L, _)) = self.margin
381
- if output is None:
382
- return radio_filtered[U : U + s0, L : L + s1]
383
- else:
384
- output[:, :] = radio_filtered[U : U + s0, L : L + s1]
385
- return output
386
-
387
- def lmicron_to_db(self, Lmicron):
388
- """
389
- Utility to convert the "Lmicron" parameter of PyHST
390
- to a value of delta/beta.
391
- Please see the doc of nabu.preproc.phase.lmicron_to_db()
392
- """
393
- return lmicron_to_db(Lmicron, self.energy_kev, self.distance_micron)
394
-
395
- __call__ = apply_filter
396
-
397
- retrieve_phase = apply_filter
398
-
399
-
400
- def compute_paganin_margin(shape, cutoff=1e3, **pag_kwargs):
401
- """
402
- Compute the convolution margin to use when calling PaganinPhaseRetrieval class.
403
-
404
- Parameters
405
- -----------
406
- shape: tuple
407
- Detector shape in the form (n_z, n_x)
408
- """
409
- P = PaganinPhaseRetrieval(shape, **pag_kwargs)
410
-
411
- ifft_func = np.fft.irfft2 if P.use_rfft else np.fft.ifft2
412
- conv_kernel = ifft_func(P.paganin_filter)
413
-
414
- vmax = conv_kernel[0, 0]
415
-
416
- v_margin = get_decay(conv_kernel[:, 0], cutoff=cutoff, vmax=vmax)
417
- h_margin = get_decay(conv_kernel[0, :], cutoff=cutoff, vmax=vmax)
418
- # If the Paganin filter is very narrow, then the corresponding convolution
419
- # kernel is constant, and np.argmax() gives 0 (when it should give the max value)
420
- if v_margin == 0:
421
- v_margin = shape[0]
422
- if h_margin == 0:
423
- h_margin = shape[1]
424
-
425
- return v_margin, h_margin
@@ -1,143 +0,0 @@
1
- import numpy as np
2
- import pycuda.driver as cuda
3
- from ..utils import get_cuda_srcfile, check_supported, docstring
4
- from ..cuda.processing import CudaProcessing
5
- from ..processing.fft_cuda import get_fft_class
6
- from .phase import PaganinPhaseRetrieval
7
-
8
-
9
- class CudaPaganinPhaseRetrieval(PaganinPhaseRetrieval):
10
- supported_paddings = ["zeros", "constant", "edge"]
11
-
12
- @docstring(PaganinPhaseRetrieval)
13
- def __init__(
14
- self,
15
- shape,
16
- distance=0.5,
17
- energy=20,
18
- delta_beta=250.0,
19
- pixel_size=1e-6,
20
- padding="edge",
21
- margin=None,
22
- cuda_options=None,
23
- fftw_num_threads=None, # COMPAT.
24
- fft_num_threads=None,
25
- fft_backend="skcuda",
26
- ):
27
- """
28
- Please refer to the documentation of
29
- nabu.preproc.phase.PaganinPhaseRetrieval
30
- """
31
- padding = self._check_padding(padding)
32
- self.cuda_processing = CudaProcessing(**(cuda_options or {}))
33
- super().__init__(
34
- shape,
35
- distance=distance,
36
- energy=energy,
37
- delta_beta=delta_beta,
38
- pixel_size=pixel_size,
39
- padding=padding,
40
- margin=margin,
41
- use_rfft=True,
42
- fft_num_threads=False,
43
- )
44
- self._init_gpu_arrays()
45
- self._init_fft(fft_backend)
46
- self._init_padding_kernel()
47
- self._init_mult_kernel()
48
-
49
- def _check_padding(self, padding):
50
- check_supported(padding, self.supported_paddings, "padding")
51
- if padding == "zeros":
52
- padding = "constant"
53
- return padding
54
-
55
- def _init_gpu_arrays(self):
56
- self.d_paganin_filter = self.cuda_processing.to_device(
57
- "d_paganin_filter", np.ascontiguousarray(self.paganin_filter, dtype=np.float32)
58
- )
59
-
60
- # overwrite parent method, don't initialize any FFT plan
61
- def _get_fft(self, use_rfft, fft_num_threads):
62
- self.use_rfft = use_rfft
63
-
64
- def _init_fft(self, fft_backend):
65
- fft_cls = get_fft_class(backend=fft_backend)
66
- self.cufft = fft_cls(shape=self.data_padded.shape, dtype=np.float32, r2c=True)
67
- self.d_radio_padded = self.cuda_processing.allocate_array("d_radio_padded", self.cufft.shape, "f")
68
- self.d_radio_f = self.cuda_processing.allocate_array("d_radio_f", self.cufft.shape_out, np.complex64)
69
-
70
- def _init_padding_kernel(self):
71
- kern_signature = {"constant": "Piiiiiiiiffff", "edge": "Piiiiiiii"}
72
- self.padding_kernel = self.cuda_processing.kernel(
73
- "padding_%s" % self.padding,
74
- filename=get_cuda_srcfile("padding.cu"),
75
- signature=kern_signature[self.padding],
76
- )
77
- Ny, Nx = self.shape
78
- Nyp, Nxp = self.shape_padded
79
- self.padding_kernel_args = [
80
- self.d_radio_padded,
81
- Nx,
82
- Ny,
83
- Nxp,
84
- Nyp,
85
- self.pad_left_len,
86
- self.pad_right_len,
87
- self.pad_top_len,
88
- self.pad_bottom_len,
89
- ]
90
- # TODO configurable constant values
91
- if self.padding == "constant":
92
- self.padding_kernel_args.extend([0, 0, 0, 0])
93
-
94
- def _init_mult_kernel(self):
95
- self.cpxmult_kernel = self.cuda_processing.kernel(
96
- "inplace_complexreal_mul_2Dby2D",
97
- filename=get_cuda_srcfile("ElementOp.cu"),
98
- signature="PPii",
99
- )
100
- self.cpxmult_kernel_args = [
101
- self.d_radio_f,
102
- self.d_paganin_filter,
103
- self.shape_padded[1] // 2 + 1,
104
- self.shape_padded[0],
105
- ]
106
-
107
- def set_input(self, data):
108
- assert data.shape == self.shape
109
- assert data.dtype == np.float32
110
- # Rectangular memcopy
111
- # TODO profile, and if needed include this copy in the padding kernel
112
- if isinstance(data, np.ndarray) or isinstance(data, self.cuda_processing.array_class):
113
- self.d_radio_padded[: self.shape[0], : self.shape[1]] = data[:, :]
114
- elif isinstance(data, cuda.DeviceAllocation):
115
- # TODO manual memcpy2D
116
- raise NotImplementedError("pycuda buffers are not supported yet")
117
- else:
118
- raise ValueError("Expected either numpy array, pycuda array or pycuda buffer")
119
-
120
- def get_output(self, output):
121
- s0, s1 = self.shape_inner
122
- ((U, _), (L, _)) = self.margin
123
- if output is None:
124
- # copy D2H
125
- return self.d_radio_padded[U : U + s0, L : L + s1].get()
126
- assert output.shape == self.shape_inner
127
- assert output.dtype == np.float32
128
- output[:, :] = self.d_radio_padded[U : U + s0, L : L + s1]
129
- return output
130
-
131
- def apply_filter(self, radio, output=None):
132
- self.set_input(radio)
133
-
134
- self.padding_kernel(*self.padding_kernel_args)
135
- self.cufft.fft(self.d_radio_padded, output=self.d_radio_f)
136
- self.cpxmult_kernel(*self.cpxmult_kernel_args)
137
- self.cufft.ifft(self.d_radio_f, output=self.d_radio_padded)
138
-
139
- return self.get_output(output)
140
-
141
- __call__ = apply_filter
142
-
143
- retrieve_phase = apply_filter
@@ -1,95 +0,0 @@
1
- from math import floor
2
- import numpy as np
3
-
4
-
5
- class VerticalShift:
6
- def __init__(self, radios_shape, shifts):
7
- """
8
- This class is used when a vertical translation (along the tomography
9
- rotation axis) occurred.
10
-
11
- These translations are meant "per projection" and can be due either to
12
- mechanical errors, or can be applied purposefully with known motor movements
13
- to smear rings artefacts.
14
-
15
- The object is initialised with an array of shifts: one shift for each projection.
16
- A positive shifts means that the axis has moved in the positive Z direction.
17
- The interpolation is done taking for a pixel (y,x) the pixel found at (y+shft,x)
18
- in the recorded images.
19
-
20
- The method apply_vertical_shifts performs the correctionson the radios.
21
-
22
- Parameters
23
- ----------
24
- radios_shape: tuple
25
- Shape of the radios chunk, in the form (n_radios, n_y, n_x)
26
- shifts: sequence of floats
27
- one shift for each projection
28
-
29
- Notes
30
- ------
31
- During the acquisition, there might be other translations, each of them
32
- orthogonal to the rotation axis.
33
- - A "horizontal" translation in the detector plane: this is handled
34
- directly in the Backprojection operation.
35
- - A translation along the beam direction: this one is of no concern
36
- for parallel-beam geometry
37
- """
38
- self.radios_shape = radios_shape
39
- self.shifts = shifts
40
- self._init_interp_coefficients()
41
-
42
- def _init_interp_coefficients(self):
43
- self.interp_infos = []
44
- for s in self.shifts:
45
- s0 = int(floor(s))
46
- f = s - s0
47
- self.interp_infos.append([s0, f])
48
-
49
- def _check(self, radios, iangles):
50
- assert np.min(iangles) >= 0
51
- assert np.max(iangles) < len(self.interp_infos)
52
- assert len(iangles) == radios.shape[0]
53
-
54
- def apply_vertical_shifts(self, radios, iangles, output=None):
55
- """
56
- Parameters
57
- ----------
58
- radios: a sequence of np.array
59
- The input radios. If the optional parameter is not given, they are modified in-place
60
- iangles: a sequence of integers
61
- Must have the same lenght as radios.
62
- It contains the index at which the shift is found in `self.shifts`
63
- given by `shifts` argument in the initialisation of the object.
64
- output: a sequence of np.array, optional
65
- If given, it will be modified to contain the shifted radios.
66
- Must be of the same shape of `radios`.
67
- """
68
- self._check(radios, iangles)
69
-
70
- newradio = np.zeros_like(radios[0])
71
- for radio, ia in zip(radios, iangles):
72
- newradio[:] = 0
73
- S0, f = self.interp_infos[ia]
74
- s0 = S0
75
-
76
- if s0 > 0:
77
- newradio[:-s0] = radio[s0:] * (1 - f)
78
- elif s0 == 0:
79
- newradio[:] = radio[s0:] * (1 - f)
80
- else:
81
- newradio[-s0:] = radio[:s0] * (1 - f)
82
-
83
- s0 = S0 + 1
84
-
85
- if s0 > 0:
86
- newradio[:-s0] += radio[s0:] * f
87
- elif s0 == 0:
88
- newradio[:] += radio[s0:] * f
89
- else:
90
- newradio[-s0:] += radio[:s0] * f
91
-
92
- if output is None:
93
- radios[ia] = newradio
94
- else:
95
- output[ia] = newradio