nabu 2024.1.1__py3-none-any.whl → 2024.1.3__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 (2097) hide show
  1. doc/doc_config.py +32 -0
  2. nabu/__init__.py +1 -1
  3. nabu/app/cast_volume.py +11 -2
  4. nabu/app/multicor.py +24 -2
  5. nabu/io/cast_volume.py +3 -3
  6. nabu/io/utils.py +2 -2
  7. nabu/reconstruction/rings_cuda.py +25 -10
  8. nabu/stitching/tests/test_z_stitching.py +0 -1
  9. nabu/stitching/z_stitching.py +3 -3
  10. {nabu-2024.1.1.dist-info → nabu-2024.1.3.dist-info}/METADATA +2 -2
  11. nabu-2024.1.3.dist-info/RECORD +296 -0
  12. nabu-2024.1.3.dist-info/top_level.txt +2 -0
  13. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/doc/conf.py +0 -137
  14. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/doc/create_conf_doc.py +0 -38
  15. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/doc/get_mathjax.py +0 -34
  16. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/__init__.py +0 -17
  17. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/__init__.py +0 -0
  18. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/bootstrap.py +0 -88
  19. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/bootstrap_stitching.py +0 -69
  20. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/cast_volume.py +0 -272
  21. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/cli_configs.py +0 -626
  22. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/compare_volumes.py +0 -94
  23. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/composite_cor.py +0 -144
  24. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/correct_rot.py +0 -70
  25. 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
  26. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/diag_to_pix.py +0 -358
  27. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/diag_to_rot.py +0 -449
  28. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/double_flatfield.py +0 -143
  29. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/generate_header.py +0 -261
  30. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/histogram.py +0 -197
  31. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/multicor.py +0 -90
  32. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/nx_z_splitter.py +0 -125
  33. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/parse_reconstruction_log.py +0 -151
  34. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/prepare_weights_double.py +0 -163
  35. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/reconstruct.py +0 -120
  36. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/reconstruct_helical.py +0 -116
  37. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/reduce_dark_flat.py +0 -181
  38. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/rotate.py +0 -162
  39. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/shrink_dataset.py +0 -98
  40. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/stitching.py +0 -85
  41. 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
  42. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/utils.py +0 -33
  43. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/validator.py +0 -110
  44. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/__init__.py +0 -0
  45. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/convolution.py +0 -8
  46. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/fft.py +0 -4
  47. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/kernel.py +0 -97
  48. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/medfilt.py +0 -6
  49. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/padding.py +0 -6
  50. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/processing.py +0 -75
  51. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/tests/__init__.py +0 -1
  52. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/utils.py +0 -331
  53. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/__init__.py +0 -12
  54. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/alignment.py +0 -578
  55. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/cor.py +0 -1621
  56. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/cor_sino.py +0 -183
  57. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/distortion.py +0 -112
  58. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/focus.py +0 -362
  59. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/__init__.py +0 -0
  60. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_alignment.py +0 -70
  61. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_cor.py +0 -472
  62. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_focus.py +0 -105
  63. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_tilt.py +0 -41
  64. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_translation.py +0 -78
  65. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tilt.py +0 -214
  66. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/translation.py +0 -193
  67. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/utils.py +0 -39
  68. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/__init__.py +0 -2
  69. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/cast_volume.py +0 -371
  70. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/detector_distortion.py +0 -305
  71. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/reader.py +0 -628
  72. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/reader_helical.py +0 -114
  73. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tests/__init__.py +0 -0
  74. 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
  75. 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
  76. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tests/test_writers.py +0 -187
  77. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tiffwriter_zmm.py +0 -99
  78. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/utils.py +0 -263
  79. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/writer.py +0 -892
  80. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/__init__.py +0 -0
  81. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/binning.py +0 -98
  82. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/fftshift.py +0 -6
  83. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/filters.py +0 -24
  84. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/fourier_filters.py +0 -152
  85. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/histogram.py +0 -6
  86. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/histogram_cuda.py +0 -8
  87. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/kernel_base.py +0 -4
  88. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/padding.py +0 -83
  89. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/padding_base.py +0 -6
  90. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/processing_base.py +0 -4
  91. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/rotation.py +0 -6
  92. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/rotation_cuda.py +0 -6
  93. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/tests/__init__.py +0 -1
  94. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/tests/test_binning.py +0 -48
  95. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/tests/test_interpolation.py +0 -70
  96. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/transpose.py +0 -6
  97. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/unsharp.py +0 -4
  98. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/unsharp_cuda.py +0 -6
  99. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/unsharp_opencl.py +0 -8
  100. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/utils.py +0 -117
  101. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/__init__.py +0 -0
  102. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/fft.py +0 -6
  103. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/kernel.py +0 -135
  104. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/memcpy.py +0 -35
  105. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/padding.py +0 -6
  106. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/processing.py +0 -62
  107. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/tests/__init__.py +0 -0
  108. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/utils.py +0 -292
  109. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/__init__.py +0 -0
  110. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/config.py +0 -265
  111. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/config_validators.py +0 -589
  112. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/datadump.py +0 -164
  113. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/dataset_validator.py +0 -211
  114. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/detector_distortion_provider.py +0 -20
  115. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/estimators.py +0 -1012
  116. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fallback_utils.py +0 -149
  117. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/__init__.py +0 -0
  118. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/chunked.py +0 -849
  119. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/chunked_cuda.py +0 -152
  120. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/computations.py +0 -260
  121. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/dataset_validator.py +0 -63
  122. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/nabu_config.py +0 -590
  123. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/processconfig.py +0 -825
  124. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/reconstruction.py +0 -851
  125. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/__init__.py +0 -0
  126. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/dataset_validator.py +0 -19
  127. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/fbp.py +0 -147
  128. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/filtering.py +0 -246
  129. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/gridded_accumulator.py +0 -575
  130. 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
  131. 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
  132. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_reconstruction.py +0 -598
  133. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_utils.py +0 -42
  134. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/nabu_config.py +0 -175
  135. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/processconfig.py +0 -62
  136. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/span_strategy.py +0 -483
  137. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/__init__.py +0 -0
  138. 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
  139. 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
  140. 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
  141. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/utils.py +0 -51
  142. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/weight_balancer.py +0 -101
  143. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/params.py +0 -163
  144. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/processconfig.py +0 -210
  145. 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
  146. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/tests/test_estimators.py +0 -149
  147. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/utils.py +0 -116
  148. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/writer.py +0 -193
  149. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/xrdct/__init__.py +0 -0
  150. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/__init__.py +0 -7
  151. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/alignment.py +0 -11
  152. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ccd.py +0 -161
  153. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ccd_cuda.py +0 -169
  154. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ctf.py +0 -361
  155. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ctf_cuda.py +0 -142
  156. 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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  1981. build/lib/nabu/preproc/flatfield_cuda.py +0 -144
  1982. build/lib/nabu/preproc/flatfield_variable_region.py +0 -79
  1983. build/lib/nabu/preproc/phase.py +0 -425
  1984. build/lib/nabu/preproc/phase_cuda.py +0 -143
  1985. build/lib/nabu/preproc/shift.py +0 -95
  1986. build/lib/nabu/preproc/shift_cuda.py +0 -102
  1987. build/lib/nabu/preproc/tests/__init__.py +0 -1
  1988. build/lib/nabu/preproc/tests/test_ccd_corr.py +0 -59
  1989. build/lib/nabu/preproc/tests/test_ctf.py +0 -250
  1990. build/lib/nabu/preproc/tests/test_double_flatfield.py +0 -86
  1991. build/lib/nabu/preproc/tests/test_flatfield.py +0 -626
  1992. build/lib/nabu/preproc/tests/test_paganin.py +0 -67
  1993. build/lib/nabu/preproc/tests/test_vshift.py +0 -73
  1994. build/lib/nabu/processing/__init__.py +0 -0
  1995. build/lib/nabu/processing/convolution_cuda.py +0 -375
  1996. build/lib/nabu/processing/fft_base.py +0 -163
  1997. build/lib/nabu/processing/fft_cuda.py +0 -256
  1998. build/lib/nabu/processing/fft_opencl.py +0 -54
  1999. build/lib/nabu/processing/fftshift.py +0 -134
  2000. build/lib/nabu/processing/histogram.py +0 -286
  2001. build/lib/nabu/processing/histogram_cuda.py +0 -103
  2002. build/lib/nabu/processing/kernel_base.py +0 -126
  2003. build/lib/nabu/processing/medfilt_cuda.py +0 -159
  2004. build/lib/nabu/processing/muladd.py +0 -29
  2005. build/lib/nabu/processing/muladd_cuda.py +0 -68
  2006. build/lib/nabu/processing/padding_base.py +0 -71
  2007. build/lib/nabu/processing/padding_cuda.py +0 -75
  2008. build/lib/nabu/processing/padding_opencl.py +0 -77
  2009. build/lib/nabu/processing/processing_base.py +0 -123
  2010. build/lib/nabu/processing/roll_opencl.py +0 -64
  2011. build/lib/nabu/processing/rotation.py +0 -63
  2012. build/lib/nabu/processing/rotation_cuda.py +0 -66
  2013. build/lib/nabu/processing/tests/__init__.py +0 -0
  2014. build/lib/nabu/processing/tests/test_fft.py +0 -268
  2015. build/lib/nabu/processing/tests/test_fftshift.py +0 -71
  2016. build/lib/nabu/processing/tests/test_histogram.py +0 -55
  2017. build/lib/nabu/processing/tests/test_medfilt.py +0 -77
  2018. build/lib/nabu/processing/tests/test_muladd.py +0 -54
  2019. build/lib/nabu/processing/tests/test_padding.py +0 -247
  2020. build/lib/nabu/processing/tests/test_roll.py +0 -63
  2021. build/lib/nabu/processing/tests/test_rotation.py +0 -83
  2022. build/lib/nabu/processing/tests/test_transpose.py +0 -72
  2023. build/lib/nabu/processing/tests/test_unsharp.py +0 -106
  2024. build/lib/nabu/processing/transpose.py +0 -126
  2025. build/lib/nabu/processing/unsharp.py +0 -79
  2026. build/lib/nabu/processing/unsharp_cuda.py +0 -53
  2027. build/lib/nabu/processing/unsharp_opencl.py +0 -75
  2028. build/lib/nabu/reconstruction/__init__.py +0 -3
  2029. build/lib/nabu/reconstruction/cone.py +0 -241
  2030. build/lib/nabu/reconstruction/fbp.py +0 -124
  2031. build/lib/nabu/reconstruction/fbp_base.py +0 -391
  2032. build/lib/nabu/reconstruction/fbp_opencl.py +0 -78
  2033. build/lib/nabu/reconstruction/filtering.py +0 -220
  2034. build/lib/nabu/reconstruction/filtering_cuda.py +0 -103
  2035. build/lib/nabu/reconstruction/filtering_opencl.py +0 -111
  2036. build/lib/nabu/reconstruction/projection.py +0 -240
  2037. build/lib/nabu/reconstruction/reconstructor.py +0 -174
  2038. build/lib/nabu/reconstruction/reconstructor_cuda.py +0 -44
  2039. build/lib/nabu/reconstruction/rings.py +0 -248
  2040. build/lib/nabu/reconstruction/rings_cuda.py +0 -322
  2041. build/lib/nabu/reconstruction/sinogram.py +0 -467
  2042. build/lib/nabu/reconstruction/sinogram_cuda.py +0 -250
  2043. build/lib/nabu/reconstruction/sinogram_opencl.py +0 -40
  2044. build/lib/nabu/reconstruction/tests/__init__.py +0 -1
  2045. build/lib/nabu/reconstruction/tests/test_cone.py +0 -308
  2046. build/lib/nabu/reconstruction/tests/test_deringer.py +0 -220
  2047. build/lib/nabu/reconstruction/tests/test_fbp.py +0 -252
  2048. build/lib/nabu/reconstruction/tests/test_filtering.py +0 -133
  2049. build/lib/nabu/reconstruction/tests/test_halftomo.py +0 -100
  2050. build/lib/nabu/reconstruction/tests/test_projector.py +0 -164
  2051. build/lib/nabu/reconstruction/tests/test_reconstructor.py +0 -93
  2052. build/lib/nabu/reconstruction/tests/test_sino_normalization.py +0 -85
  2053. build/lib/nabu/resources/__init__.py +0 -0
  2054. build/lib/nabu/resources/cli/__init__.py +0 -0
  2055. build/lib/nabu/resources/cor.py +0 -5
  2056. build/lib/nabu/resources/dataset_analyzer.py +0 -469
  2057. build/lib/nabu/resources/gpu.py +0 -169
  2058. build/lib/nabu/resources/logger.py +0 -130
  2059. build/lib/nabu/resources/nxflatfield.py +0 -217
  2060. build/lib/nabu/resources/templates/__init__.py +0 -0
  2061. build/lib/nabu/resources/tests/__init__.py +0 -0
  2062. build/lib/nabu/resources/tests/test_nxflatfield.py +0 -104
  2063. build/lib/nabu/resources/tests/test_units.py +0 -47
  2064. build/lib/nabu/resources/utils.py +0 -174
  2065. build/lib/nabu/stitching/__init__.py +0 -0
  2066. build/lib/nabu/stitching/alignment.py +0 -184
  2067. build/lib/nabu/stitching/config.py +0 -1286
  2068. build/lib/nabu/stitching/definitions.py +0 -6
  2069. build/lib/nabu/stitching/frame_composition.py +0 -155
  2070. build/lib/nabu/stitching/overlap.py +0 -373
  2071. build/lib/nabu/stitching/sample_normalization.py +0 -60
  2072. build/lib/nabu/stitching/slurm_utils.py +0 -204
  2073. build/lib/nabu/stitching/tests/__init__.py +0 -0
  2074. build/lib/nabu/stitching/tests/test_alignment.py +0 -99
  2075. build/lib/nabu/stitching/tests/test_config.py +0 -226
  2076. build/lib/nabu/stitching/tests/test_frame_composition.py +0 -180
  2077. build/lib/nabu/stitching/tests/test_overlap.py +0 -98
  2078. build/lib/nabu/stitching/tests/test_sample_normalization.py +0 -49
  2079. build/lib/nabu/stitching/tests/test_slurm_utils.py +0 -146
  2080. build/lib/nabu/stitching/tests/test_utils.py +0 -21
  2081. build/lib/nabu/stitching/tests/test_z_stitching.py +0 -1183
  2082. build/lib/nabu/stitching/utils.py +0 -563
  2083. build/lib/nabu/stitching/z_stitching.py +0 -2279
  2084. build/lib/nabu/tests.py +0 -51
  2085. build/lib/nabu/testutils.py +0 -375
  2086. build/lib/nabu/thirdparty/__init__.py +0 -0
  2087. build/lib/nabu/thirdparty/algotom_convert_sino.py +0 -276
  2088. build/lib/nabu/thirdparty/pore3d_deringer_munch.py +0 -108
  2089. build/lib/nabu/thirdparty/tomocupy_remove_stripe.py +0 -586
  2090. build/lib/nabu/thirdparty/tomopy_phase.py +0 -239
  2091. build/lib/nabu/thirdparty/tomwer_load_flats_darks.py +0 -162
  2092. build/lib/nabu/utils.py +0 -836
  2093. nabu-2024.1.1.dist-info/RECORD +0 -2375
  2094. nabu-2024.1.1.dist-info/top_level.txt +0 -4
  2095. {nabu-2024.1.1.dist-info → nabu-2024.1.3.dist-info}/LICENSE +0 -0
  2096. {nabu-2024.1.1.dist-info → nabu-2024.1.3.dist-info}/WHEEL +0 -0
  2097. {nabu-2024.1.1.dist-info → nabu-2024.1.3.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