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
  155. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/double_flatfield.py +0 -212
  156. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/double_flatfield_cuda.py +0 -174
  157. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/double_flatfield_variable_region.py +0 -68
  158. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/flatfield.py +0 -448
  159. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/flatfield_cuda.py +0 -144
  160. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/flatfield_variable_region.py +0 -79
  161. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/phase.py +0 -425
  162. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/phase_cuda.py +0 -143
  163. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/shift.py +0 -95
  164. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/shift_cuda.py +0 -102
  165. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/tests/__init__.py +0 -1
  166. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/tests/test_ccd_corr.py +0 -59
  167. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/tests/test_ctf.py +0 -250
  168. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/tests/test_double_flatfield.py +0 -86
  169. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/tests/test_flatfield.py +0 -626
  170. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/tests/test_paganin.py +0 -67
  171. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/tests/test_vshift.py +0 -73
  172. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/__init__.py +0 -0
  173. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/convolution_cuda.py +0 -375
  174. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/fft_base.py +0 -163
  175. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/fft_cuda.py +0 -256
  176. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/fft_opencl.py +0 -54
  177. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/fftshift.py +0 -134
  178. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/histogram.py +0 -286
  179. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/histogram_cuda.py +0 -103
  180. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/kernel_base.py +0 -126
  181. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/medfilt_cuda.py +0 -159
  182. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/muladd.py +0 -29
  183. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/muladd_cuda.py +0 -68
  184. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/padding_base.py +0 -71
  185. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/padding_cuda.py +0 -75
  186. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/padding_opencl.py +0 -77
  187. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/processing_base.py +0 -123
  188. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/roll_opencl.py +0 -64
  189. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/rotation.py +0 -63
  190. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/rotation_cuda.py +0 -66
  191. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/__init__.py +0 -0
  192. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_fft.py +0 -268
  193. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_fftshift.py +0 -71
  194. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_histogram.py +0 -55
  195. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_medfilt.py +0 -77
  196. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_muladd.py +0 -54
  197. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_padding.py +0 -247
  198. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_roll.py +0 -63
  199. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_rotation.py +0 -83
  200. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_transpose.py +0 -72
  201. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_unsharp.py +0 -106
  202. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/transpose.py +0 -126
  203. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/unsharp.py +0 -79
  204. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/unsharp_cuda.py +0 -53
  205. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/unsharp_opencl.py +0 -75
  206. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/__init__.py +0 -3
  207. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/cone.py +0 -241
  208. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/fbp.py +0 -124
  209. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/fbp_base.py +0 -391
  210. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/fbp_opencl.py +0 -78
  211. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/filtering.py +0 -220
  212. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/filtering_cuda.py +0 -103
  213. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/filtering_opencl.py +0 -111
  214. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/projection.py +0 -240
  215. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/reconstructor.py +0 -174
  216. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/reconstructor_cuda.py +0 -44
  217. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/rings.py +0 -248
  218. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/rings_cuda.py +0 -322
  219. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/sinogram.py +0 -467
  220. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/sinogram_cuda.py +0 -250
  221. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/sinogram_opencl.py +0 -40
  222. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/__init__.py +0 -1
  223. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_cone.py +0 -308
  224. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_deringer.py +0 -220
  225. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_fbp.py +0 -252
  226. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_filtering.py +0 -133
  227. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_halftomo.py +0 -100
  228. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_projector.py +0 -164
  229. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_reconstructor.py +0 -93
  230. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_sino_normalization.py +0 -85
  231. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/__init__.py +0 -0
  232. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/cli/__init__.py +0 -0
  233. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/cor.py +0 -5
  234. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/dataset_analyzer.py +0 -469
  235. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/gpu.py +0 -169
  236. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/logger.py +0 -130
  237. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/nxflatfield.py +0 -217
  238. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/templates/__init__.py +0 -0
  239. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/tests/__init__.py +0 -0
  240. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/tests/test_nxflatfield.py +0 -104
  241. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/tests/test_units.py +0 -47
  242. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/utils.py +0 -174
  243. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/__init__.py +0 -0
  244. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/alignment.py +0 -184
  245. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/config.py +0 -1286
  246. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/definitions.py +0 -6
  247. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/frame_composition.py +0 -155
  248. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/overlap.py +0 -373
  249. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/sample_normalization.py +0 -60
  250. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/slurm_utils.py +0 -204
  251. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/__init__.py +0 -0
  252. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_alignment.py +0 -99
  253. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_config.py +0 -226
  254. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_frame_composition.py +0 -180
  255. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_overlap.py +0 -98
  256. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_sample_normalization.py +0 -49
  257. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_slurm_utils.py +0 -146
  258. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_utils.py +0 -21
  259. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_z_stitching.py +0 -1183
  260. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/utils.py +0 -563
  261. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/z_stitching.py +0 -2279
  262. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/tests.py +0 -51
  263. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/testutils.py +0 -375
  264. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/thirdparty/__init__.py +0 -0
  265. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/thirdparty/algotom_convert_sino.py +0 -276
  266. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/thirdparty/pore3d_deringer_munch.py +0 -108
  267. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/thirdparty/tomocupy_remove_stripe.py +0 -586
  268. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/thirdparty/tomopy_phase.py +0 -239
  269. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/thirdparty/tomwer_load_flats_darks.py +0 -162
  270. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/utils.py +0 -836
  271. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/doc/conf.py +0 -137
  272. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/doc/create_conf_doc.py +0 -38
  273. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/doc/get_mathjax.py +0 -34
  274. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/__init__.py +0 -17
  275. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/__init__.py +0 -0
  276. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/bootstrap.py +0 -88
  277. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/bootstrap_stitching.py +0 -69
  278. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/cast_volume.py +0 -272
  279. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/cli_configs.py +0 -626
  280. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/compare_volumes.py +0 -94
  281. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/composite_cor.py +0 -144
  282. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/correct_rot.py +0 -70
  283. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/create_distortion_map_from_poly.py +0 -153
  284. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/diag_to_pix.py +0 -358
  285. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/diag_to_rot.py +0 -449
  286. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/double_flatfield.py +0 -143
  287. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/generate_header.py +0 -261
  288. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/histogram.py +0 -197
  289. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/multicor.py +0 -90
  290. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/nx_z_splitter.py +0 -125
  291. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/parse_reconstruction_log.py +0 -151
  292. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/prepare_weights_double.py +0 -163
  293. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/reconstruct.py +0 -120
  294. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/reconstruct_helical.py +0 -116
  295. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/reduce_dark_flat.py +0 -181
  296. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/rotate.py +0 -162
  297. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/shrink_dataset.py +0 -98
  298. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/stitching.py +0 -85
  299. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/tests/test_reduce_dark_flat.py +0 -78
  300. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/utils.py +0 -33
  301. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/validator.py +0 -110
  302. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/__init__.py +0 -0
  303. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/convolution.py +0 -8
  304. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/fft.py +0 -4
  305. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/kernel.py +0 -97
  306. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/medfilt.py +0 -6
  307. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/padding.py +0 -6
  308. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/processing.py +0 -75
  309. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/tests/__init__.py +0 -1
  310. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/utils.py +0 -331
  311. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/__init__.py +0 -12
  312. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/alignment.py +0 -578
  313. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/cor.py +0 -1621
  314. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/cor_sino.py +0 -183
  315. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/distortion.py +0 -112
  316. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/focus.py +0 -362
  317. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/__init__.py +0 -0
  318. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_alignment.py +0 -70
  319. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_cor.py +0 -472
  320. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_focus.py +0 -105
  321. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_tilt.py +0 -41
  322. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_translation.py +0 -78
  323. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tilt.py +0 -214
  324. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/translation.py +0 -193
  325. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/utils.py +0 -39
  326. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/__init__.py +0 -2
  327. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/cast_volume.py +0 -371
  328. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/detector_distortion.py +0 -305
  329. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/reader.py +0 -628
  330. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/reader_helical.py +0 -114
  331. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tests/__init__.py +0 -0
  332. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tests/test_cast_volume.py +0 -339
  333. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tests/test_detector_distortion.py +0 -178
  334. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tests/test_writers.py +0 -187
  335. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tiffwriter_zmm.py +0 -99
  336. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/utils.py +0 -263
  337. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/writer.py +0 -892
  338. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/__init__.py +0 -0
  339. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/binning.py +0 -98
  340. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/fftshift.py +0 -6
  341. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/filters.py +0 -24
  342. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/fourier_filters.py +0 -152
  343. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/histogram.py +0 -6
  344. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/histogram_cuda.py +0 -8
  345. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/kernel_base.py +0 -4
  346. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/padding.py +0 -83
  347. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/padding_base.py +0 -6
  348. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/processing_base.py +0 -4
  349. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/rotation.py +0 -6
  350. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/rotation_cuda.py +0 -6
  351. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/tests/__init__.py +0 -1
  352. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/tests/test_binning.py +0 -48
  353. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/tests/test_interpolation.py +0 -70
  354. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/transpose.py +0 -6
  355. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/unsharp.py +0 -4
  356. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/unsharp_cuda.py +0 -6
  357. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/unsharp_opencl.py +0 -8
  358. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/utils.py +0 -117
  359. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/__init__.py +0 -0
  360. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/fft.py +0 -6
  361. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/kernel.py +0 -135
  362. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/memcpy.py +0 -35
  363. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/padding.py +0 -6
  364. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/processing.py +0 -62
  365. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/tests/__init__.py +0 -0
  366. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/utils.py +0 -292
  367. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/__init__.py +0 -0
  368. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/config.py +0 -265
  369. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/config_validators.py +0 -589
  370. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/datadump.py +0 -164
  371. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/dataset_validator.py +0 -211
  372. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/detector_distortion_provider.py +0 -20
  373. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/estimators.py +0 -1012
  374. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fallback_utils.py +0 -149
  375. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/__init__.py +0 -0
  376. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/chunked.py +0 -849
  377. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/chunked_cuda.py +0 -152
  378. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/computations.py +0 -260
  379. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/dataset_validator.py +0 -63
  380. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/nabu_config.py +0 -590
  381. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/processconfig.py +0 -825
  382. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/reconstruction.py +0 -851
  383. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/__init__.py +0 -0
  384. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/dataset_validator.py +0 -19
  385. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/fbp.py +0 -147
  386. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/filtering.py +0 -246
  387. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/gridded_accumulator.py +0 -575
  388. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_chunked_regridded.py +0 -1670
  389. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_chunked_regridded_cuda.py +0 -119
  390. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_reconstruction.py +0 -598
  391. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_utils.py +0 -42
  392. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/nabu_config.py +0 -175
  393. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/processconfig.py +0 -62
  394. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/span_strategy.py +0 -483
  395. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/__init__.py +0 -0
  396. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/test_accumulator.py +0 -157
  397. 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
  398. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/test_strategy.py +0 -61
  399. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/utils.py +0 -51
  400. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/weight_balancer.py +0 -101
  401. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/params.py +0 -163
  402. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/processconfig.py +0 -210
  403. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/tests/test_chunk_reader.py +0 -78
  404. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/tests/test_estimators.py +0 -149
  405. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/utils.py +0 -116
  406. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/writer.py +0 -193
  407. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/xrdct/__init__.py +0 -0
  408. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/__init__.py +0 -7
  409. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/alignment.py +0 -11
  410. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ccd.py +0 -161
  411. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ccd_cuda.py +0 -169
  412. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ctf.py +0 -361
  413. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ctf_cuda.py +0 -142
  414. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/distortion.py +0 -92
  415. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/double_flatfield.py +0 -212
  416. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/double_flatfield_cuda.py +0 -174
  417. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/double_flatfield_variable_region.py +0 -68
  418. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/flatfield.py +0 -448
  419. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/flatfield_cuda.py +0 -144
  420. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/flatfield_variable_region.py +0 -79
  421. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/phase.py +0 -425
  422. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/phase_cuda.py +0 -143
  423. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/shift.py +0 -95
  424. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/shift_cuda.py +0 -102
  425. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/tests/__init__.py +0 -1
  426. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/tests/test_ccd_corr.py +0 -59
  427. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/tests/test_ctf.py +0 -250
  428. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/tests/test_double_flatfield.py +0 -86
  429. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/tests/test_flatfield.py +0 -626
  430. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/tests/test_paganin.py +0 -67
  431. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/tests/test_vshift.py +0 -73
  432. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/__init__.py +0 -0
  433. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/convolution_cuda.py +0 -375
  434. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/fft_base.py +0 -163
  435. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/fft_cuda.py +0 -256
  436. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/fft_opencl.py +0 -54
  437. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/fftshift.py +0 -134
  438. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/histogram.py +0 -286
  439. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/histogram_cuda.py +0 -103
  440. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/kernel_base.py +0 -126
  441. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/medfilt_cuda.py +0 -159
  442. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/muladd.py +0 -29
  443. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/muladd_cuda.py +0 -68
  444. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/padding_base.py +0 -71
  445. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/padding_cuda.py +0 -75
  446. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/padding_opencl.py +0 -77
  447. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/processing_base.py +0 -123
  448. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/roll_opencl.py +0 -64
  449. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/rotation.py +0 -63
  450. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/rotation_cuda.py +0 -66
  451. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/__init__.py +0 -0
  452. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_fft.py +0 -268
  453. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_fftshift.py +0 -71
  454. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_histogram.py +0 -55
  455. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_medfilt.py +0 -77
  456. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_muladd.py +0 -54
  457. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_padding.py +0 -247
  458. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_roll.py +0 -63
  459. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_rotation.py +0 -83
  460. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_transpose.py +0 -72
  461. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_unsharp.py +0 -106
  462. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/transpose.py +0 -126
  463. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/unsharp.py +0 -79
  464. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/unsharp_cuda.py +0 -53
  465. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/unsharp_opencl.py +0 -75
  466. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/__init__.py +0 -3
  467. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/cone.py +0 -241
  468. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/fbp.py +0 -124
  469. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/fbp_base.py +0 -391
  470. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/fbp_opencl.py +0 -78
  471. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/filtering.py +0 -220
  472. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/filtering_cuda.py +0 -103
  473. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/filtering_opencl.py +0 -111
  474. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/projection.py +0 -240
  475. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/reconstructor.py +0 -174
  476. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/reconstructor_cuda.py +0 -44
  477. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/rings.py +0 -248
  478. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/rings_cuda.py +0 -322
  479. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/sinogram.py +0 -467
  480. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/sinogram_cuda.py +0 -250
  481. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/sinogram_opencl.py +0 -40
  482. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/__init__.py +0 -1
  483. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_cone.py +0 -308
  484. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_deringer.py +0 -220
  485. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_fbp.py +0 -252
  486. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_filtering.py +0 -133
  487. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_halftomo.py +0 -100
  488. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_projector.py +0 -164
  489. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_reconstructor.py +0 -93
  490. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_sino_normalization.py +0 -85
  491. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/__init__.py +0 -0
  492. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/cli/__init__.py +0 -0
  493. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/cor.py +0 -5
  494. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/dataset_analyzer.py +0 -469
  495. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/gpu.py +0 -169
  496. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/logger.py +0 -130
  497. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/nxflatfield.py +0 -217
  498. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/templates/__init__.py +0 -0
  499. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/tests/__init__.py +0 -0
  500. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/tests/test_nxflatfield.py +0 -104
  501. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/tests/test_units.py +0 -47
  502. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/utils.py +0 -174
  503. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/__init__.py +0 -0
  504. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/alignment.py +0 -184
  505. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/config.py +0 -1286
  506. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/definitions.py +0 -6
  507. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/frame_composition.py +0 -155
  508. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/overlap.py +0 -373
  509. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/sample_normalization.py +0 -60
  510. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/slurm_utils.py +0 -204
  511. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/__init__.py +0 -0
  512. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_alignment.py +0 -99
  513. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_config.py +0 -226
  514. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_frame_composition.py +0 -180
  515. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_overlap.py +0 -98
  516. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_sample_normalization.py +0 -49
  517. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_slurm_utils.py +0 -146
  518. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_utils.py +0 -21
  519. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_z_stitching.py +0 -1183
  520. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/utils.py +0 -563
  521. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/z_stitching.py +0 -2279
  522. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/tests.py +0 -51
  523. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/testutils.py +0 -375
  524. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/thirdparty/__init__.py +0 -0
  525. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/thirdparty/algotom_convert_sino.py +0 -276
  526. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/thirdparty/pore3d_deringer_munch.py +0 -108
  527. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/thirdparty/tomocupy_remove_stripe.py +0 -586
  528. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/thirdparty/tomopy_phase.py +0 -239
  529. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/thirdparty/tomwer_load_flats_darks.py +0 -162
  530. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/utils.py +0 -836
  531. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/doc/conf.py +0 -137
  532. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/doc/create_conf_doc.py +0 -38
  533. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/doc/get_mathjax.py +0 -34
  534. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/__init__.py +0 -17
  535. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/__init__.py +0 -0
  536. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/bootstrap.py +0 -88
  537. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/bootstrap_stitching.py +0 -69
  538. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/cast_volume.py +0 -272
  539. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/cli_configs.py +0 -626
  540. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/compare_volumes.py +0 -94
  541. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/composite_cor.py +0 -144
  542. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/correct_rot.py +0 -70
  543. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/create_distortion_map_from_poly.py +0 -153
  544. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/diag_to_pix.py +0 -358
  545. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/diag_to_rot.py +0 -449
  546. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/double_flatfield.py +0 -143
  547. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/generate_header.py +0 -261
  548. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/histogram.py +0 -197
  549. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/multicor.py +0 -90
  550. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/nx_z_splitter.py +0 -125
  551. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/parse_reconstruction_log.py +0 -151
  552. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/prepare_weights_double.py +0 -163
  553. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/reconstruct.py +0 -120
  554. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/reconstruct_helical.py +0 -116
  555. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/reduce_dark_flat.py +0 -181
  556. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/rotate.py +0 -162
  557. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/shrink_dataset.py +0 -98
  558. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/stitching.py +0 -85
  559. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/tests/test_reduce_dark_flat.py +0 -78
  560. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/utils.py +0 -33
  561. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/validator.py +0 -110
  562. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/__init__.py +0 -0
  563. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/convolution.py +0 -8
  564. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/fft.py +0 -4
  565. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/kernel.py +0 -97
  566. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/medfilt.py +0 -6
  567. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/padding.py +0 -6
  568. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/processing.py +0 -75
  569. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/tests/__init__.py +0 -1
  570. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/utils.py +0 -331
  571. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/__init__.py +0 -12
  572. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/alignment.py +0 -578
  573. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/cor.py +0 -1621
  574. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/cor_sino.py +0 -183
  575. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/distortion.py +0 -112
  576. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/focus.py +0 -362
  577. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/__init__.py +0 -0
  578. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_alignment.py +0 -70
  579. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_cor.py +0 -472
  580. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_focus.py +0 -105
  581. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_tilt.py +0 -41
  582. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_translation.py +0 -78
  583. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tilt.py +0 -214
  584. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/translation.py +0 -193
  585. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/utils.py +0 -39
  586. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/__init__.py +0 -2
  587. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/cast_volume.py +0 -371
  588. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/detector_distortion.py +0 -305
  589. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/reader.py +0 -628
  590. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/reader_helical.py +0 -114
  591. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tests/__init__.py +0 -0
  592. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tests/test_cast_volume.py +0 -339
  593. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tests/test_detector_distortion.py +0 -178
  594. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tests/test_writers.py +0 -187
  595. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tiffwriter_zmm.py +0 -99
  596. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/utils.py +0 -263
  597. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/writer.py +0 -892
  598. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/__init__.py +0 -0
  599. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/binning.py +0 -98
  600. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/fftshift.py +0 -6
  601. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/filters.py +0 -24
  602. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/fourier_filters.py +0 -152
  603. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/histogram.py +0 -6
  604. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/histogram_cuda.py +0 -8
  605. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/kernel_base.py +0 -4
  606. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/padding.py +0 -83
  607. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/padding_base.py +0 -6
  608. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/processing_base.py +0 -4
  609. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/rotation.py +0 -6
  610. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/rotation_cuda.py +0 -6
  611. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/tests/__init__.py +0 -1
  612. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/tests/test_binning.py +0 -48
  613. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/tests/test_interpolation.py +0 -70
  614. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/transpose.py +0 -6
  615. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/unsharp.py +0 -4
  616. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/unsharp_cuda.py +0 -6
  617. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/unsharp_opencl.py +0 -8
  618. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/utils.py +0 -117
  619. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/__init__.py +0 -0
  620. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/fft.py +0 -6
  621. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/kernel.py +0 -135
  622. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/memcpy.py +0 -35
  623. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/padding.py +0 -6
  624. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/processing.py +0 -62
  625. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/tests/__init__.py +0 -0
  626. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/utils.py +0 -292
  627. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/__init__.py +0 -0
  628. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/config.py +0 -265
  629. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/config_validators.py +0 -589
  630. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/datadump.py +0 -164
  631. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/dataset_validator.py +0 -211
  632. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/detector_distortion_provider.py +0 -20
  633. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/estimators.py +0 -1012
  634. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fallback_utils.py +0 -149
  635. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/__init__.py +0 -0
  636. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/chunked.py +0 -849
  637. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/chunked_cuda.py +0 -152
  638. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/computations.py +0 -260
  639. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/dataset_validator.py +0 -63
  640. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/nabu_config.py +0 -590
  641. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/processconfig.py +0 -825
  642. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/reconstruction.py +0 -851
  643. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/__init__.py +0 -0
  644. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/dataset_validator.py +0 -19
  645. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/fbp.py +0 -147
  646. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/filtering.py +0 -246
  647. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/gridded_accumulator.py +0 -575
  648. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_chunked_regridded.py +0 -1670
  649. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_chunked_regridded_cuda.py +0 -119
  650. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_reconstruction.py +0 -598
  651. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_utils.py +0 -42
  652. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/nabu_config.py +0 -175
  653. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/processconfig.py +0 -62
  654. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/span_strategy.py +0 -483
  655. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/__init__.py +0 -0
  656. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/test_accumulator.py +0 -157
  657. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/test_pipeline_elements_full.py +0 -355
  658. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/test_strategy.py +0 -61
  659. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/utils.py +0 -51
  660. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/weight_balancer.py +0 -101
  661. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/params.py +0 -163
  662. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/processconfig.py +0 -210
  663. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/tests/test_chunk_reader.py +0 -78
  664. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/tests/test_estimators.py +0 -149
  665. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/utils.py +0 -116
  666. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/writer.py +0 -193
  667. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/xrdct/__init__.py +0 -0
  668. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/__init__.py +0 -7
  669. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/alignment.py +0 -11
  670. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ccd.py +0 -161
  671. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ccd_cuda.py +0 -169
  672. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ctf.py +0 -361
  673. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ctf_cuda.py +0 -142
  674. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/distortion.py +0 -92
  675. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/double_flatfield.py +0 -212
  676. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/double_flatfield_cuda.py +0 -174
  677. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/double_flatfield_variable_region.py +0 -68
  678. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/flatfield.py +0 -448
  679. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/flatfield_cuda.py +0 -144
  680. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/flatfield_variable_region.py +0 -79
  681. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/phase.py +0 -425
  682. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/phase_cuda.py +0 -143
  683. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/shift.py +0 -95
  684. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/shift_cuda.py +0 -102
  685. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/tests/__init__.py +0 -1
  686. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/tests/test_ccd_corr.py +0 -59
  687. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/tests/test_ctf.py +0 -250
  688. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/tests/test_double_flatfield.py +0 -86
  689. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/tests/test_flatfield.py +0 -626
  690. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/tests/test_paganin.py +0 -67
  691. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/tests/test_vshift.py +0 -73
  692. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/__init__.py +0 -0
  693. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/convolution_cuda.py +0 -375
  694. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/fft_base.py +0 -163
  695. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/fft_cuda.py +0 -256
  696. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/fft_opencl.py +0 -54
  697. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/fftshift.py +0 -134
  698. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/histogram.py +0 -286
  699. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/histogram_cuda.py +0 -103
  700. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/kernel_base.py +0 -126
  701. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/medfilt_cuda.py +0 -159
  702. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/muladd.py +0 -29
  703. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/muladd_cuda.py +0 -68
  704. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/padding_base.py +0 -71
  705. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/padding_cuda.py +0 -75
  706. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/padding_opencl.py +0 -77
  707. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/processing_base.py +0 -123
  708. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/roll_opencl.py +0 -64
  709. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/rotation.py +0 -63
  710. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/rotation_cuda.py +0 -66
  711. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/__init__.py +0 -0
  712. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_fft.py +0 -268
  713. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_fftshift.py +0 -71
  714. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_histogram.py +0 -55
  715. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_medfilt.py +0 -77
  716. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_muladd.py +0 -54
  717. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_padding.py +0 -247
  718. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_roll.py +0 -63
  719. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_rotation.py +0 -83
  720. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_transpose.py +0 -72
  721. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_unsharp.py +0 -106
  722. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/transpose.py +0 -126
  723. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/unsharp.py +0 -79
  724. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/unsharp_cuda.py +0 -53
  725. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/unsharp_opencl.py +0 -75
  726. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/__init__.py +0 -3
  727. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/cone.py +0 -241
  728. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/fbp.py +0 -124
  729. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/fbp_base.py +0 -391
  730. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/fbp_opencl.py +0 -78
  731. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/filtering.py +0 -220
  732. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/filtering_cuda.py +0 -103
  733. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/filtering_opencl.py +0 -111
  734. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/projection.py +0 -240
  735. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/reconstructor.py +0 -174
  736. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/reconstructor_cuda.py +0 -44
  737. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/rings.py +0 -248
  738. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/rings_cuda.py +0 -322
  739. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/sinogram.py +0 -467
  740. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/sinogram_cuda.py +0 -250
  741. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/sinogram_opencl.py +0 -40
  742. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/__init__.py +0 -1
  743. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_cone.py +0 -308
  744. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_deringer.py +0 -220
  745. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_fbp.py +0 -252
  746. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_filtering.py +0 -133
  747. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_halftomo.py +0 -100
  748. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_projector.py +0 -164
  749. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_reconstructor.py +0 -93
  750. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_sino_normalization.py +0 -85
  751. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/__init__.py +0 -0
  752. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/cli/__init__.py +0 -0
  753. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/cor.py +0 -5
  754. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/dataset_analyzer.py +0 -469
  755. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/gpu.py +0 -169
  756. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/logger.py +0 -130
  757. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/nxflatfield.py +0 -217
  758. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/templates/__init__.py +0 -0
  759. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/tests/__init__.py +0 -0
  760. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/tests/test_nxflatfield.py +0 -104
  761. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/tests/test_units.py +0 -47
  762. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/utils.py +0 -174
  763. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/__init__.py +0 -0
  764. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/alignment.py +0 -184
  765. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/config.py +0 -1286
  766. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/definitions.py +0 -6
  767. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/frame_composition.py +0 -155
  768. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/overlap.py +0 -373
  769. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/sample_normalization.py +0 -60
  770. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/slurm_utils.py +0 -204
  771. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/__init__.py +0 -0
  772. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_alignment.py +0 -99
  773. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_config.py +0 -226
  774. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_frame_composition.py +0 -180
  775. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_overlap.py +0 -98
  776. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_sample_normalization.py +0 -49
  777. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_slurm_utils.py +0 -146
  778. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_utils.py +0 -21
  779. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_z_stitching.py +0 -1183
  780. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/utils.py +0 -563
  781. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/z_stitching.py +0 -2279
  782. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/tests.py +0 -51
  783. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/testutils.py +0 -375
  784. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/thirdparty/__init__.py +0 -0
  785. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/thirdparty/algotom_convert_sino.py +0 -276
  786. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/thirdparty/pore3d_deringer_munch.py +0 -108
  787. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/thirdparty/tomocupy_remove_stripe.py +0 -586
  788. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/thirdparty/tomopy_phase.py +0 -239
  789. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/thirdparty/tomwer_load_flats_darks.py +0 -162
  790. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/utils.py +0 -836
  791. build/lib/build/lib/build/lib/build/lib/build/lib/doc/conf.py +0 -137
  792. build/lib/build/lib/build/lib/build/lib/build/lib/doc/create_conf_doc.py +0 -38
  793. build/lib/build/lib/build/lib/build/lib/build/lib/doc/get_mathjax.py +0 -34
  794. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/__init__.py +0 -17
  795. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/__init__.py +0 -0
  796. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/bootstrap.py +0 -88
  797. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/bootstrap_stitching.py +0 -69
  798. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/cast_volume.py +0 -272
  799. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/cli_configs.py +0 -626
  800. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/compare_volumes.py +0 -94
  801. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/composite_cor.py +0 -144
  802. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/correct_rot.py +0 -70
  803. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/create_distortion_map_from_poly.py +0 -153
  804. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/diag_to_pix.py +0 -358
  805. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/diag_to_rot.py +0 -449
  806. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/double_flatfield.py +0 -143
  807. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/generate_header.py +0 -261
  808. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/histogram.py +0 -197
  809. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/multicor.py +0 -90
  810. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/nx_z_splitter.py +0 -125
  811. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/parse_reconstruction_log.py +0 -151
  812. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/prepare_weights_double.py +0 -163
  813. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/reconstruct.py +0 -120
  814. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/reconstruct_helical.py +0 -116
  815. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/reduce_dark_flat.py +0 -181
  816. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/rotate.py +0 -162
  817. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/shrink_dataset.py +0 -98
  818. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/stitching.py +0 -85
  819. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/tests/test_reduce_dark_flat.py +0 -78
  820. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/utils.py +0 -33
  821. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/validator.py +0 -110
  822. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/__init__.py +0 -0
  823. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/convolution.py +0 -8
  824. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/fft.py +0 -4
  825. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/kernel.py +0 -97
  826. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/medfilt.py +0 -6
  827. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/padding.py +0 -6
  828. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/processing.py +0 -75
  829. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/tests/__init__.py +0 -1
  830. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/utils.py +0 -331
  831. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/__init__.py +0 -12
  832. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/alignment.py +0 -578
  833. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/cor.py +0 -1621
  834. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/cor_sino.py +0 -183
  835. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/distortion.py +0 -112
  836. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/focus.py +0 -362
  837. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/__init__.py +0 -0
  838. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_alignment.py +0 -70
  839. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_cor.py +0 -472
  840. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_focus.py +0 -105
  841. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_tilt.py +0 -41
  842. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_translation.py +0 -78
  843. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tilt.py +0 -214
  844. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/translation.py +0 -193
  845. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/utils.py +0 -39
  846. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/__init__.py +0 -2
  847. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/cast_volume.py +0 -371
  848. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/detector_distortion.py +0 -305
  849. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/reader.py +0 -628
  850. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/reader_helical.py +0 -114
  851. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tests/__init__.py +0 -0
  852. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tests/test_cast_volume.py +0 -339
  853. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tests/test_detector_distortion.py +0 -178
  854. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tests/test_writers.py +0 -187
  855. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tiffwriter_zmm.py +0 -99
  856. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/utils.py +0 -263
  857. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/writer.py +0 -892
  858. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/__init__.py +0 -0
  859. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/binning.py +0 -98
  860. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/fftshift.py +0 -6
  861. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/filters.py +0 -24
  862. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/fourier_filters.py +0 -152
  863. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/histogram.py +0 -6
  864. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/histogram_cuda.py +0 -8
  865. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/kernel_base.py +0 -4
  866. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/padding.py +0 -83
  867. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/padding_base.py +0 -6
  868. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/processing_base.py +0 -4
  869. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/rotation.py +0 -6
  870. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/rotation_cuda.py +0 -6
  871. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/tests/__init__.py +0 -1
  872. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/tests/test_binning.py +0 -48
  873. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/tests/test_interpolation.py +0 -70
  874. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/transpose.py +0 -6
  875. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/unsharp.py +0 -4
  876. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/unsharp_cuda.py +0 -6
  877. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/unsharp_opencl.py +0 -8
  878. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/utils.py +0 -117
  879. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/__init__.py +0 -0
  880. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/fft.py +0 -6
  881. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/kernel.py +0 -135
  882. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/memcpy.py +0 -35
  883. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/padding.py +0 -6
  884. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/processing.py +0 -62
  885. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/tests/__init__.py +0 -0
  886. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/utils.py +0 -292
  887. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/__init__.py +0 -0
  888. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/config.py +0 -265
  889. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/config_validators.py +0 -589
  890. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/datadump.py +0 -164
  891. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/dataset_validator.py +0 -211
  892. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/detector_distortion_provider.py +0 -20
  893. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/estimators.py +0 -1012
  894. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fallback_utils.py +0 -149
  895. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/__init__.py +0 -0
  896. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/chunked.py +0 -849
  897. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/chunked_cuda.py +0 -152
  898. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/computations.py +0 -260
  899. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/dataset_validator.py +0 -63
  900. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/nabu_config.py +0 -590
  901. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/processconfig.py +0 -825
  902. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/reconstruction.py +0 -851
  903. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/__init__.py +0 -0
  904. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/dataset_validator.py +0 -19
  905. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/fbp.py +0 -147
  906. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/filtering.py +0 -246
  907. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/gridded_accumulator.py +0 -575
  908. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_chunked_regridded.py +0 -1670
  909. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_chunked_regridded_cuda.py +0 -119
  910. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_reconstruction.py +0 -598
  911. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_utils.py +0 -42
  912. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/nabu_config.py +0 -175
  913. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/processconfig.py +0 -62
  914. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/span_strategy.py +0 -483
  915. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/__init__.py +0 -0
  916. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/test_accumulator.py +0 -157
  917. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/test_pipeline_elements_full.py +0 -355
  918. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/test_strategy.py +0 -61
  919. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/utils.py +0 -51
  920. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/weight_balancer.py +0 -101
  921. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/params.py +0 -163
  922. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/processconfig.py +0 -210
  923. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/tests/test_chunk_reader.py +0 -78
  924. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/tests/test_estimators.py +0 -149
  925. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/utils.py +0 -116
  926. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/writer.py +0 -193
  927. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/xrdct/__init__.py +0 -0
  928. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/__init__.py +0 -7
  929. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/alignment.py +0 -11
  930. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ccd.py +0 -161
  931. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ccd_cuda.py +0 -169
  932. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ctf.py +0 -361
  933. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ctf_cuda.py +0 -142
  934. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/distortion.py +0 -92
  935. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/double_flatfield.py +0 -212
  936. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/double_flatfield_cuda.py +0 -174
  937. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/double_flatfield_variable_region.py +0 -68
  938. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/flatfield.py +0 -448
  939. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/flatfield_cuda.py +0 -144
  940. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/flatfield_variable_region.py +0 -79
  941. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/phase.py +0 -425
  942. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/phase_cuda.py +0 -143
  943. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/shift.py +0 -95
  944. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/shift_cuda.py +0 -102
  945. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/tests/__init__.py +0 -1
  946. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/tests/test_ccd_corr.py +0 -59
  947. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/tests/test_ctf.py +0 -250
  948. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/tests/test_double_flatfield.py +0 -86
  949. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/tests/test_flatfield.py +0 -626
  950. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/tests/test_paganin.py +0 -67
  951. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/tests/test_vshift.py +0 -73
  952. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/__init__.py +0 -0
  953. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/convolution_cuda.py +0 -375
  954. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/fft_base.py +0 -163
  955. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/fft_cuda.py +0 -256
  956. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/fft_opencl.py +0 -54
  957. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/fftshift.py +0 -134
  958. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/histogram.py +0 -286
  959. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/histogram_cuda.py +0 -103
  960. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/kernel_base.py +0 -126
  961. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/medfilt_cuda.py +0 -159
  962. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/muladd.py +0 -29
  963. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/muladd_cuda.py +0 -68
  964. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/padding_base.py +0 -71
  965. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/padding_cuda.py +0 -75
  966. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/padding_opencl.py +0 -77
  967. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/processing_base.py +0 -123
  968. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/roll_opencl.py +0 -64
  969. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/rotation.py +0 -63
  970. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/rotation_cuda.py +0 -66
  971. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/__init__.py +0 -0
  972. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_fft.py +0 -268
  973. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_fftshift.py +0 -71
  974. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_histogram.py +0 -55
  975. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_medfilt.py +0 -77
  976. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_muladd.py +0 -54
  977. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_padding.py +0 -247
  978. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_roll.py +0 -63
  979. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_rotation.py +0 -83
  980. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_transpose.py +0 -72
  981. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_unsharp.py +0 -106
  982. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/transpose.py +0 -126
  983. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/unsharp.py +0 -79
  984. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/unsharp_cuda.py +0 -53
  985. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/processing/unsharp_opencl.py +0 -75
  986. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/__init__.py +0 -3
  987. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/cone.py +0 -241
  988. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/fbp.py +0 -124
  989. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/fbp_base.py +0 -391
  990. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/fbp_opencl.py +0 -78
  991. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/filtering.py +0 -220
  992. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/filtering_cuda.py +0 -103
  993. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/filtering_opencl.py +0 -111
  994. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/projection.py +0 -240
  995. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/reconstructor.py +0 -174
  996. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/reconstructor_cuda.py +0 -44
  997. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/rings.py +0 -248
  998. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/rings_cuda.py +0 -322
  999. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/sinogram.py +0 -467
  1000. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/sinogram_cuda.py +0 -250
  1001. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/sinogram_opencl.py +0 -40
  1002. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/__init__.py +0 -1
  1003. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_cone.py +0 -308
  1004. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_deringer.py +0 -220
  1005. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_fbp.py +0 -252
  1006. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_filtering.py +0 -133
  1007. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_halftomo.py +0 -100
  1008. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_projector.py +0 -164
  1009. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_reconstructor.py +0 -93
  1010. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_sino_normalization.py +0 -85
  1011. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/__init__.py +0 -0
  1012. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/cli/__init__.py +0 -0
  1013. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/cor.py +0 -5
  1014. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/dataset_analyzer.py +0 -469
  1015. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/gpu.py +0 -169
  1016. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/logger.py +0 -130
  1017. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/nxflatfield.py +0 -217
  1018. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/templates/__init__.py +0 -0
  1019. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/tests/__init__.py +0 -0
  1020. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/tests/test_nxflatfield.py +0 -104
  1021. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/tests/test_units.py +0 -47
  1022. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/resources/utils.py +0 -174
  1023. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/__init__.py +0 -0
  1024. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/alignment.py +0 -184
  1025. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/config.py +0 -1286
  1026. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/definitions.py +0 -6
  1027. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/frame_composition.py +0 -155
  1028. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/overlap.py +0 -373
  1029. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/sample_normalization.py +0 -60
  1030. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/slurm_utils.py +0 -204
  1031. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/__init__.py +0 -0
  1032. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_alignment.py +0 -99
  1033. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_config.py +0 -226
  1034. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_frame_composition.py +0 -180
  1035. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_overlap.py +0 -98
  1036. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_sample_normalization.py +0 -49
  1037. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_slurm_utils.py +0 -146
  1038. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_utils.py +0 -21
  1039. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_z_stitching.py +0 -1183
  1040. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/utils.py +0 -563
  1041. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/z_stitching.py +0 -2279
  1042. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/tests.py +0 -51
  1043. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/testutils.py +0 -375
  1044. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/thirdparty/__init__.py +0 -0
  1045. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/thirdparty/algotom_convert_sino.py +0 -276
  1046. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/thirdparty/pore3d_deringer_munch.py +0 -108
  1047. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/thirdparty/tomocupy_remove_stripe.py +0 -586
  1048. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/thirdparty/tomopy_phase.py +0 -239
  1049. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/thirdparty/tomwer_load_flats_darks.py +0 -162
  1050. build/lib/build/lib/build/lib/build/lib/build/lib/nabu/utils.py +0 -836
  1051. build/lib/build/lib/build/lib/build/lib/doc/conf.py +0 -137
  1052. build/lib/build/lib/build/lib/build/lib/doc/create_conf_doc.py +0 -38
  1053. build/lib/build/lib/build/lib/build/lib/doc/get_mathjax.py +0 -34
  1054. build/lib/build/lib/build/lib/build/lib/nabu/__init__.py +0 -17
  1055. build/lib/build/lib/build/lib/build/lib/nabu/app/__init__.py +0 -0
  1056. build/lib/build/lib/build/lib/build/lib/nabu/app/bootstrap.py +0 -88
  1057. build/lib/build/lib/build/lib/build/lib/nabu/app/bootstrap_stitching.py +0 -69
  1058. build/lib/build/lib/build/lib/build/lib/nabu/app/cast_volume.py +0 -272
  1059. build/lib/build/lib/build/lib/build/lib/nabu/app/cli_configs.py +0 -626
  1060. build/lib/build/lib/build/lib/build/lib/nabu/app/compare_volumes.py +0 -94
  1061. build/lib/build/lib/build/lib/build/lib/nabu/app/composite_cor.py +0 -144
  1062. build/lib/build/lib/build/lib/build/lib/nabu/app/correct_rot.py +0 -70
  1063. build/lib/build/lib/build/lib/build/lib/nabu/app/create_distortion_map_from_poly.py +0 -153
  1064. build/lib/build/lib/build/lib/build/lib/nabu/app/diag_to_pix.py +0 -358
  1065. build/lib/build/lib/build/lib/build/lib/nabu/app/diag_to_rot.py +0 -449
  1066. build/lib/build/lib/build/lib/build/lib/nabu/app/double_flatfield.py +0 -143
  1067. build/lib/build/lib/build/lib/build/lib/nabu/app/generate_header.py +0 -261
  1068. build/lib/build/lib/build/lib/build/lib/nabu/app/histogram.py +0 -197
  1069. build/lib/build/lib/build/lib/build/lib/nabu/app/multicor.py +0 -90
  1070. build/lib/build/lib/build/lib/build/lib/nabu/app/nx_z_splitter.py +0 -125
  1071. build/lib/build/lib/build/lib/build/lib/nabu/app/parse_reconstruction_log.py +0 -151
  1072. build/lib/build/lib/build/lib/build/lib/nabu/app/prepare_weights_double.py +0 -163
  1073. build/lib/build/lib/build/lib/build/lib/nabu/app/reconstruct.py +0 -120
  1074. build/lib/build/lib/build/lib/build/lib/nabu/app/reconstruct_helical.py +0 -116
  1075. build/lib/build/lib/build/lib/build/lib/nabu/app/reduce_dark_flat.py +0 -181
  1076. build/lib/build/lib/build/lib/build/lib/nabu/app/rotate.py +0 -162
  1077. build/lib/build/lib/build/lib/build/lib/nabu/app/shrink_dataset.py +0 -98
  1078. build/lib/build/lib/build/lib/build/lib/nabu/app/stitching.py +0 -85
  1079. build/lib/build/lib/build/lib/build/lib/nabu/app/tests/test_reduce_dark_flat.py +0 -78
  1080. build/lib/build/lib/build/lib/build/lib/nabu/app/utils.py +0 -33
  1081. build/lib/build/lib/build/lib/build/lib/nabu/app/validator.py +0 -110
  1082. build/lib/build/lib/build/lib/build/lib/nabu/cuda/__init__.py +0 -0
  1083. build/lib/build/lib/build/lib/build/lib/nabu/cuda/convolution.py +0 -8
  1084. build/lib/build/lib/build/lib/build/lib/nabu/cuda/fft.py +0 -4
  1085. build/lib/build/lib/build/lib/build/lib/nabu/cuda/kernel.py +0 -97
  1086. build/lib/build/lib/build/lib/build/lib/nabu/cuda/medfilt.py +0 -6
  1087. build/lib/build/lib/build/lib/build/lib/nabu/cuda/padding.py +0 -6
  1088. build/lib/build/lib/build/lib/build/lib/nabu/cuda/processing.py +0 -75
  1089. build/lib/build/lib/build/lib/build/lib/nabu/cuda/tests/__init__.py +0 -1
  1090. build/lib/build/lib/build/lib/build/lib/nabu/cuda/utils.py +0 -331
  1091. build/lib/build/lib/build/lib/build/lib/nabu/estimation/__init__.py +0 -12
  1092. build/lib/build/lib/build/lib/build/lib/nabu/estimation/alignment.py +0 -578
  1093. build/lib/build/lib/build/lib/build/lib/nabu/estimation/cor.py +0 -1621
  1094. build/lib/build/lib/build/lib/build/lib/nabu/estimation/cor_sino.py +0 -183
  1095. build/lib/build/lib/build/lib/build/lib/nabu/estimation/distortion.py +0 -112
  1096. build/lib/build/lib/build/lib/build/lib/nabu/estimation/focus.py +0 -362
  1097. build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/__init__.py +0 -0
  1098. build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_alignment.py +0 -70
  1099. build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_cor.py +0 -472
  1100. build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_focus.py +0 -105
  1101. build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_tilt.py +0 -41
  1102. build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_translation.py +0 -78
  1103. build/lib/build/lib/build/lib/build/lib/nabu/estimation/tilt.py +0 -214
  1104. build/lib/build/lib/build/lib/build/lib/nabu/estimation/translation.py +0 -193
  1105. build/lib/build/lib/build/lib/build/lib/nabu/estimation/utils.py +0 -39
  1106. build/lib/build/lib/build/lib/build/lib/nabu/io/__init__.py +0 -2
  1107. build/lib/build/lib/build/lib/build/lib/nabu/io/cast_volume.py +0 -371
  1108. build/lib/build/lib/build/lib/build/lib/nabu/io/detector_distortion.py +0 -305
  1109. build/lib/build/lib/build/lib/build/lib/nabu/io/reader.py +0 -628
  1110. build/lib/build/lib/build/lib/build/lib/nabu/io/reader_helical.py +0 -114
  1111. build/lib/build/lib/build/lib/build/lib/nabu/io/tests/__init__.py +0 -0
  1112. build/lib/build/lib/build/lib/build/lib/nabu/io/tests/test_cast_volume.py +0 -339
  1113. build/lib/build/lib/build/lib/build/lib/nabu/io/tests/test_detector_distortion.py +0 -178
  1114. build/lib/build/lib/build/lib/build/lib/nabu/io/tests/test_writers.py +0 -187
  1115. build/lib/build/lib/build/lib/build/lib/nabu/io/tiffwriter_zmm.py +0 -99
  1116. build/lib/build/lib/build/lib/build/lib/nabu/io/utils.py +0 -263
  1117. build/lib/build/lib/build/lib/build/lib/nabu/io/writer.py +0 -892
  1118. build/lib/build/lib/build/lib/build/lib/nabu/misc/__init__.py +0 -0
  1119. build/lib/build/lib/build/lib/build/lib/nabu/misc/binning.py +0 -98
  1120. build/lib/build/lib/build/lib/build/lib/nabu/misc/fftshift.py +0 -6
  1121. build/lib/build/lib/build/lib/build/lib/nabu/misc/filters.py +0 -24
  1122. build/lib/build/lib/build/lib/build/lib/nabu/misc/fourier_filters.py +0 -152
  1123. build/lib/build/lib/build/lib/build/lib/nabu/misc/histogram.py +0 -6
  1124. build/lib/build/lib/build/lib/build/lib/nabu/misc/histogram_cuda.py +0 -8
  1125. build/lib/build/lib/build/lib/build/lib/nabu/misc/kernel_base.py +0 -4
  1126. build/lib/build/lib/build/lib/build/lib/nabu/misc/padding.py +0 -83
  1127. build/lib/build/lib/build/lib/build/lib/nabu/misc/padding_base.py +0 -6
  1128. build/lib/build/lib/build/lib/build/lib/nabu/misc/processing_base.py +0 -4
  1129. build/lib/build/lib/build/lib/build/lib/nabu/misc/rotation.py +0 -6
  1130. build/lib/build/lib/build/lib/build/lib/nabu/misc/rotation_cuda.py +0 -6
  1131. build/lib/build/lib/build/lib/build/lib/nabu/misc/tests/__init__.py +0 -1
  1132. build/lib/build/lib/build/lib/build/lib/nabu/misc/tests/test_binning.py +0 -48
  1133. build/lib/build/lib/build/lib/build/lib/nabu/misc/tests/test_interpolation.py +0 -70
  1134. build/lib/build/lib/build/lib/build/lib/nabu/misc/transpose.py +0 -6
  1135. build/lib/build/lib/build/lib/build/lib/nabu/misc/unsharp.py +0 -4
  1136. build/lib/build/lib/build/lib/build/lib/nabu/misc/unsharp_cuda.py +0 -6
  1137. build/lib/build/lib/build/lib/build/lib/nabu/misc/unsharp_opencl.py +0 -8
  1138. build/lib/build/lib/build/lib/build/lib/nabu/misc/utils.py +0 -117
  1139. build/lib/build/lib/build/lib/build/lib/nabu/opencl/__init__.py +0 -0
  1140. build/lib/build/lib/build/lib/build/lib/nabu/opencl/fft.py +0 -6
  1141. build/lib/build/lib/build/lib/build/lib/nabu/opencl/kernel.py +0 -135
  1142. build/lib/build/lib/build/lib/build/lib/nabu/opencl/memcpy.py +0 -35
  1143. build/lib/build/lib/build/lib/build/lib/nabu/opencl/padding.py +0 -6
  1144. build/lib/build/lib/build/lib/build/lib/nabu/opencl/processing.py +0 -62
  1145. build/lib/build/lib/build/lib/build/lib/nabu/opencl/tests/__init__.py +0 -0
  1146. build/lib/build/lib/build/lib/build/lib/nabu/opencl/utils.py +0 -292
  1147. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/__init__.py +0 -0
  1148. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/config.py +0 -265
  1149. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/config_validators.py +0 -589
  1150. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/datadump.py +0 -164
  1151. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/dataset_validator.py +0 -211
  1152. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/detector_distortion_provider.py +0 -20
  1153. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/estimators.py +0 -1012
  1154. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fallback_utils.py +0 -149
  1155. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/__init__.py +0 -0
  1156. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/chunked.py +0 -849
  1157. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/chunked_cuda.py +0 -152
  1158. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/computations.py +0 -260
  1159. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/dataset_validator.py +0 -63
  1160. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/nabu_config.py +0 -590
  1161. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/processconfig.py +0 -825
  1162. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/reconstruction.py +0 -851
  1163. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/__init__.py +0 -0
  1164. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/dataset_validator.py +0 -19
  1165. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/fbp.py +0 -147
  1166. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/filtering.py +0 -246
  1167. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/gridded_accumulator.py +0 -575
  1168. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_chunked_regridded.py +0 -1670
  1169. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_chunked_regridded_cuda.py +0 -119
  1170. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_reconstruction.py +0 -598
  1171. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_utils.py +0 -42
  1172. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/nabu_config.py +0 -175
  1173. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/processconfig.py +0 -62
  1174. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/span_strategy.py +0 -483
  1175. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/__init__.py +0 -0
  1176. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/test_accumulator.py +0 -157
  1177. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/test_pipeline_elements_full.py +0 -355
  1178. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/test_strategy.py +0 -61
  1179. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/utils.py +0 -51
  1180. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/weight_balancer.py +0 -101
  1181. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/params.py +0 -163
  1182. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/processconfig.py +0 -210
  1183. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/tests/test_chunk_reader.py +0 -78
  1184. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/tests/test_estimators.py +0 -149
  1185. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/utils.py +0 -116
  1186. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/writer.py +0 -193
  1187. build/lib/build/lib/build/lib/build/lib/nabu/pipeline/xrdct/__init__.py +0 -0
  1188. build/lib/build/lib/build/lib/build/lib/nabu/preproc/__init__.py +0 -7
  1189. build/lib/build/lib/build/lib/build/lib/nabu/preproc/alignment.py +0 -11
  1190. build/lib/build/lib/build/lib/build/lib/nabu/preproc/ccd.py +0 -161
  1191. build/lib/build/lib/build/lib/build/lib/nabu/preproc/ccd_cuda.py +0 -169
  1192. build/lib/build/lib/build/lib/build/lib/nabu/preproc/ctf.py +0 -361
  1193. build/lib/build/lib/build/lib/build/lib/nabu/preproc/ctf_cuda.py +0 -142
  1194. build/lib/build/lib/build/lib/build/lib/nabu/preproc/distortion.py +0 -92
  1195. build/lib/build/lib/build/lib/build/lib/nabu/preproc/double_flatfield.py +0 -212
  1196. build/lib/build/lib/build/lib/build/lib/nabu/preproc/double_flatfield_cuda.py +0 -174
  1197. build/lib/build/lib/build/lib/build/lib/nabu/preproc/double_flatfield_variable_region.py +0 -68
  1198. build/lib/build/lib/build/lib/build/lib/nabu/preproc/flatfield.py +0 -448
  1199. build/lib/build/lib/build/lib/build/lib/nabu/preproc/flatfield_cuda.py +0 -144
  1200. build/lib/build/lib/build/lib/build/lib/nabu/preproc/flatfield_variable_region.py +0 -79
  1201. build/lib/build/lib/build/lib/build/lib/nabu/preproc/phase.py +0 -425
  1202. build/lib/build/lib/build/lib/build/lib/nabu/preproc/phase_cuda.py +0 -143
  1203. build/lib/build/lib/build/lib/build/lib/nabu/preproc/shift.py +0 -95
  1204. build/lib/build/lib/build/lib/build/lib/nabu/preproc/shift_cuda.py +0 -102
  1205. build/lib/build/lib/build/lib/build/lib/nabu/preproc/tests/__init__.py +0 -1
  1206. build/lib/build/lib/build/lib/build/lib/nabu/preproc/tests/test_ccd_corr.py +0 -59
  1207. build/lib/build/lib/build/lib/build/lib/nabu/preproc/tests/test_ctf.py +0 -250
  1208. build/lib/build/lib/build/lib/build/lib/nabu/preproc/tests/test_double_flatfield.py +0 -86
  1209. build/lib/build/lib/build/lib/build/lib/nabu/preproc/tests/test_flatfield.py +0 -626
  1210. build/lib/build/lib/build/lib/build/lib/nabu/preproc/tests/test_paganin.py +0 -67
  1211. build/lib/build/lib/build/lib/build/lib/nabu/preproc/tests/test_vshift.py +0 -73
  1212. build/lib/build/lib/build/lib/build/lib/nabu/processing/__init__.py +0 -0
  1213. build/lib/build/lib/build/lib/build/lib/nabu/processing/convolution_cuda.py +0 -375
  1214. build/lib/build/lib/build/lib/build/lib/nabu/processing/fft_base.py +0 -163
  1215. build/lib/build/lib/build/lib/build/lib/nabu/processing/fft_cuda.py +0 -256
  1216. build/lib/build/lib/build/lib/build/lib/nabu/processing/fft_opencl.py +0 -54
  1217. build/lib/build/lib/build/lib/build/lib/nabu/processing/fftshift.py +0 -134
  1218. build/lib/build/lib/build/lib/build/lib/nabu/processing/histogram.py +0 -286
  1219. build/lib/build/lib/build/lib/build/lib/nabu/processing/histogram_cuda.py +0 -103
  1220. build/lib/build/lib/build/lib/build/lib/nabu/processing/kernel_base.py +0 -126
  1221. build/lib/build/lib/build/lib/build/lib/nabu/processing/medfilt_cuda.py +0 -159
  1222. build/lib/build/lib/build/lib/build/lib/nabu/processing/muladd.py +0 -29
  1223. build/lib/build/lib/build/lib/build/lib/nabu/processing/muladd_cuda.py +0 -68
  1224. build/lib/build/lib/build/lib/build/lib/nabu/processing/padding_base.py +0 -71
  1225. build/lib/build/lib/build/lib/build/lib/nabu/processing/padding_cuda.py +0 -75
  1226. build/lib/build/lib/build/lib/build/lib/nabu/processing/padding_opencl.py +0 -77
  1227. build/lib/build/lib/build/lib/build/lib/nabu/processing/processing_base.py +0 -123
  1228. build/lib/build/lib/build/lib/build/lib/nabu/processing/roll_opencl.py +0 -64
  1229. build/lib/build/lib/build/lib/build/lib/nabu/processing/rotation.py +0 -63
  1230. build/lib/build/lib/build/lib/build/lib/nabu/processing/rotation_cuda.py +0 -66
  1231. build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/__init__.py +0 -0
  1232. build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_fft.py +0 -268
  1233. build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_fftshift.py +0 -71
  1234. build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_histogram.py +0 -55
  1235. build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_medfilt.py +0 -77
  1236. build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_muladd.py +0 -54
  1237. build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_padding.py +0 -247
  1238. build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_roll.py +0 -63
  1239. build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_rotation.py +0 -83
  1240. build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_transpose.py +0 -72
  1241. build/lib/build/lib/build/lib/build/lib/nabu/processing/tests/test_unsharp.py +0 -106
  1242. build/lib/build/lib/build/lib/build/lib/nabu/processing/transpose.py +0 -126
  1243. build/lib/build/lib/build/lib/build/lib/nabu/processing/unsharp.py +0 -79
  1244. build/lib/build/lib/build/lib/build/lib/nabu/processing/unsharp_cuda.py +0 -53
  1245. build/lib/build/lib/build/lib/build/lib/nabu/processing/unsharp_opencl.py +0 -75
  1246. build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/__init__.py +0 -3
  1247. build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/cone.py +0 -241
  1248. build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/fbp.py +0 -124
  1249. build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/fbp_base.py +0 -391
  1250. build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/fbp_opencl.py +0 -78
  1251. build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/filtering.py +0 -220
  1252. build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/filtering_cuda.py +0 -103
  1253. build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/filtering_opencl.py +0 -111
  1254. build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/projection.py +0 -240
  1255. build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/reconstructor.py +0 -174
  1256. build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/reconstructor_cuda.py +0 -44
  1257. build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/rings.py +0 -248
  1258. build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/rings_cuda.py +0 -322
  1259. build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/sinogram.py +0 -467
  1260. build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/sinogram_cuda.py +0 -250
  1261. build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/sinogram_opencl.py +0 -40
  1262. build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/__init__.py +0 -1
  1263. build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_cone.py +0 -308
  1264. build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_deringer.py +0 -220
  1265. build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_fbp.py +0 -252
  1266. build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_filtering.py +0 -133
  1267. build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_halftomo.py +0 -100
  1268. build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_projector.py +0 -164
  1269. build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_reconstructor.py +0 -93
  1270. build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_sino_normalization.py +0 -85
  1271. build/lib/build/lib/build/lib/build/lib/nabu/resources/__init__.py +0 -0
  1272. build/lib/build/lib/build/lib/build/lib/nabu/resources/cli/__init__.py +0 -0
  1273. build/lib/build/lib/build/lib/build/lib/nabu/resources/cor.py +0 -5
  1274. build/lib/build/lib/build/lib/build/lib/nabu/resources/dataset_analyzer.py +0 -469
  1275. build/lib/build/lib/build/lib/build/lib/nabu/resources/gpu.py +0 -169
  1276. build/lib/build/lib/build/lib/build/lib/nabu/resources/logger.py +0 -130
  1277. build/lib/build/lib/build/lib/build/lib/nabu/resources/nxflatfield.py +0 -217
  1278. build/lib/build/lib/build/lib/build/lib/nabu/resources/templates/__init__.py +0 -0
  1279. build/lib/build/lib/build/lib/build/lib/nabu/resources/tests/__init__.py +0 -0
  1280. build/lib/build/lib/build/lib/build/lib/nabu/resources/tests/test_nxflatfield.py +0 -104
  1281. build/lib/build/lib/build/lib/build/lib/nabu/resources/tests/test_units.py +0 -47
  1282. build/lib/build/lib/build/lib/build/lib/nabu/resources/utils.py +0 -174
  1283. build/lib/build/lib/build/lib/build/lib/nabu/stitching/__init__.py +0 -0
  1284. build/lib/build/lib/build/lib/build/lib/nabu/stitching/alignment.py +0 -184
  1285. build/lib/build/lib/build/lib/build/lib/nabu/stitching/config.py +0 -1286
  1286. build/lib/build/lib/build/lib/build/lib/nabu/stitching/definitions.py +0 -6
  1287. build/lib/build/lib/build/lib/build/lib/nabu/stitching/frame_composition.py +0 -155
  1288. build/lib/build/lib/build/lib/build/lib/nabu/stitching/overlap.py +0 -373
  1289. build/lib/build/lib/build/lib/build/lib/nabu/stitching/sample_normalization.py +0 -60
  1290. build/lib/build/lib/build/lib/build/lib/nabu/stitching/slurm_utils.py +0 -204
  1291. build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/__init__.py +0 -0
  1292. build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_alignment.py +0 -99
  1293. build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_config.py +0 -226
  1294. build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_frame_composition.py +0 -180
  1295. build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_overlap.py +0 -98
  1296. build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_sample_normalization.py +0 -49
  1297. build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_slurm_utils.py +0 -146
  1298. build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_utils.py +0 -21
  1299. build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_z_stitching.py +0 -1183
  1300. build/lib/build/lib/build/lib/build/lib/nabu/stitching/utils.py +0 -563
  1301. build/lib/build/lib/build/lib/build/lib/nabu/stitching/z_stitching.py +0 -2279
  1302. build/lib/build/lib/build/lib/build/lib/nabu/tests.py +0 -51
  1303. build/lib/build/lib/build/lib/build/lib/nabu/testutils.py +0 -375
  1304. build/lib/build/lib/build/lib/build/lib/nabu/thirdparty/__init__.py +0 -0
  1305. build/lib/build/lib/build/lib/build/lib/nabu/thirdparty/algotom_convert_sino.py +0 -276
  1306. build/lib/build/lib/build/lib/build/lib/nabu/thirdparty/pore3d_deringer_munch.py +0 -108
  1307. build/lib/build/lib/build/lib/build/lib/nabu/thirdparty/tomocupy_remove_stripe.py +0 -586
  1308. build/lib/build/lib/build/lib/build/lib/nabu/thirdparty/tomopy_phase.py +0 -239
  1309. build/lib/build/lib/build/lib/build/lib/nabu/thirdparty/tomwer_load_flats_darks.py +0 -162
  1310. build/lib/build/lib/build/lib/build/lib/nabu/utils.py +0 -836
  1311. build/lib/build/lib/build/lib/doc/conf.py +0 -137
  1312. build/lib/build/lib/build/lib/doc/create_conf_doc.py +0 -38
  1313. build/lib/build/lib/build/lib/doc/get_mathjax.py +0 -34
  1314. build/lib/build/lib/build/lib/nabu/__init__.py +0 -17
  1315. build/lib/build/lib/build/lib/nabu/app/__init__.py +0 -0
  1316. build/lib/build/lib/build/lib/nabu/app/bootstrap.py +0 -88
  1317. build/lib/build/lib/build/lib/nabu/app/bootstrap_stitching.py +0 -69
  1318. build/lib/build/lib/build/lib/nabu/app/cast_volume.py +0 -272
  1319. build/lib/build/lib/build/lib/nabu/app/cli_configs.py +0 -626
  1320. build/lib/build/lib/build/lib/nabu/app/compare_volumes.py +0 -94
  1321. build/lib/build/lib/build/lib/nabu/app/composite_cor.py +0 -144
  1322. build/lib/build/lib/build/lib/nabu/app/correct_rot.py +0 -70
  1323. build/lib/build/lib/build/lib/nabu/app/create_distortion_map_from_poly.py +0 -153
  1324. build/lib/build/lib/build/lib/nabu/app/diag_to_pix.py +0 -358
  1325. build/lib/build/lib/build/lib/nabu/app/diag_to_rot.py +0 -449
  1326. build/lib/build/lib/build/lib/nabu/app/double_flatfield.py +0 -143
  1327. build/lib/build/lib/build/lib/nabu/app/generate_header.py +0 -261
  1328. build/lib/build/lib/build/lib/nabu/app/histogram.py +0 -197
  1329. build/lib/build/lib/build/lib/nabu/app/multicor.py +0 -90
  1330. build/lib/build/lib/build/lib/nabu/app/nx_z_splitter.py +0 -125
  1331. build/lib/build/lib/build/lib/nabu/app/parse_reconstruction_log.py +0 -151
  1332. build/lib/build/lib/build/lib/nabu/app/prepare_weights_double.py +0 -163
  1333. build/lib/build/lib/build/lib/nabu/app/reconstruct.py +0 -120
  1334. build/lib/build/lib/build/lib/nabu/app/reconstruct_helical.py +0 -116
  1335. build/lib/build/lib/build/lib/nabu/app/reduce_dark_flat.py +0 -181
  1336. build/lib/build/lib/build/lib/nabu/app/rotate.py +0 -162
  1337. build/lib/build/lib/build/lib/nabu/app/shrink_dataset.py +0 -98
  1338. build/lib/build/lib/build/lib/nabu/app/stitching.py +0 -85
  1339. build/lib/build/lib/build/lib/nabu/app/tests/test_reduce_dark_flat.py +0 -78
  1340. build/lib/build/lib/build/lib/nabu/app/utils.py +0 -33
  1341. build/lib/build/lib/build/lib/nabu/app/validator.py +0 -110
  1342. build/lib/build/lib/build/lib/nabu/cuda/__init__.py +0 -0
  1343. build/lib/build/lib/build/lib/nabu/cuda/convolution.py +0 -8
  1344. build/lib/build/lib/build/lib/nabu/cuda/fft.py +0 -4
  1345. build/lib/build/lib/build/lib/nabu/cuda/kernel.py +0 -97
  1346. build/lib/build/lib/build/lib/nabu/cuda/medfilt.py +0 -6
  1347. build/lib/build/lib/build/lib/nabu/cuda/padding.py +0 -6
  1348. build/lib/build/lib/build/lib/nabu/cuda/processing.py +0 -75
  1349. build/lib/build/lib/build/lib/nabu/cuda/tests/__init__.py +0 -1
  1350. build/lib/build/lib/build/lib/nabu/cuda/utils.py +0 -331
  1351. build/lib/build/lib/build/lib/nabu/estimation/__init__.py +0 -12
  1352. build/lib/build/lib/build/lib/nabu/estimation/alignment.py +0 -578
  1353. build/lib/build/lib/build/lib/nabu/estimation/cor.py +0 -1621
  1354. build/lib/build/lib/build/lib/nabu/estimation/cor_sino.py +0 -183
  1355. build/lib/build/lib/build/lib/nabu/estimation/distortion.py +0 -112
  1356. build/lib/build/lib/build/lib/nabu/estimation/focus.py +0 -362
  1357. build/lib/build/lib/build/lib/nabu/estimation/tests/__init__.py +0 -0
  1358. build/lib/build/lib/build/lib/nabu/estimation/tests/test_alignment.py +0 -70
  1359. build/lib/build/lib/build/lib/nabu/estimation/tests/test_cor.py +0 -472
  1360. build/lib/build/lib/build/lib/nabu/estimation/tests/test_focus.py +0 -105
  1361. build/lib/build/lib/build/lib/nabu/estimation/tests/test_tilt.py +0 -41
  1362. build/lib/build/lib/build/lib/nabu/estimation/tests/test_translation.py +0 -78
  1363. build/lib/build/lib/build/lib/nabu/estimation/tilt.py +0 -214
  1364. build/lib/build/lib/build/lib/nabu/estimation/translation.py +0 -193
  1365. build/lib/build/lib/build/lib/nabu/estimation/utils.py +0 -39
  1366. build/lib/build/lib/build/lib/nabu/io/__init__.py +0 -2
  1367. build/lib/build/lib/build/lib/nabu/io/cast_volume.py +0 -371
  1368. build/lib/build/lib/build/lib/nabu/io/detector_distortion.py +0 -305
  1369. build/lib/build/lib/build/lib/nabu/io/reader.py +0 -628
  1370. build/lib/build/lib/build/lib/nabu/io/reader_helical.py +0 -114
  1371. build/lib/build/lib/build/lib/nabu/io/tests/__init__.py +0 -0
  1372. build/lib/build/lib/build/lib/nabu/io/tests/test_cast_volume.py +0 -339
  1373. build/lib/build/lib/build/lib/nabu/io/tests/test_detector_distortion.py +0 -178
  1374. build/lib/build/lib/build/lib/nabu/io/tests/test_writers.py +0 -187
  1375. build/lib/build/lib/build/lib/nabu/io/tiffwriter_zmm.py +0 -99
  1376. build/lib/build/lib/build/lib/nabu/io/utils.py +0 -263
  1377. build/lib/build/lib/build/lib/nabu/io/writer.py +0 -892
  1378. build/lib/build/lib/build/lib/nabu/misc/__init__.py +0 -0
  1379. build/lib/build/lib/build/lib/nabu/misc/binning.py +0 -98
  1380. build/lib/build/lib/build/lib/nabu/misc/fftshift.py +0 -6
  1381. build/lib/build/lib/build/lib/nabu/misc/filters.py +0 -24
  1382. build/lib/build/lib/build/lib/nabu/misc/fourier_filters.py +0 -152
  1383. build/lib/build/lib/build/lib/nabu/misc/histogram.py +0 -6
  1384. build/lib/build/lib/build/lib/nabu/misc/histogram_cuda.py +0 -8
  1385. build/lib/build/lib/build/lib/nabu/misc/kernel_base.py +0 -4
  1386. build/lib/build/lib/build/lib/nabu/misc/padding.py +0 -83
  1387. build/lib/build/lib/build/lib/nabu/misc/padding_base.py +0 -6
  1388. build/lib/build/lib/build/lib/nabu/misc/processing_base.py +0 -4
  1389. build/lib/build/lib/build/lib/nabu/misc/rotation.py +0 -6
  1390. build/lib/build/lib/build/lib/nabu/misc/rotation_cuda.py +0 -6
  1391. build/lib/build/lib/build/lib/nabu/misc/tests/__init__.py +0 -1
  1392. build/lib/build/lib/build/lib/nabu/misc/tests/test_binning.py +0 -48
  1393. build/lib/build/lib/build/lib/nabu/misc/tests/test_interpolation.py +0 -70
  1394. build/lib/build/lib/build/lib/nabu/misc/transpose.py +0 -6
  1395. build/lib/build/lib/build/lib/nabu/misc/unsharp.py +0 -4
  1396. build/lib/build/lib/build/lib/nabu/misc/unsharp_cuda.py +0 -6
  1397. build/lib/build/lib/build/lib/nabu/misc/unsharp_opencl.py +0 -8
  1398. build/lib/build/lib/build/lib/nabu/misc/utils.py +0 -117
  1399. build/lib/build/lib/build/lib/nabu/opencl/__init__.py +0 -0
  1400. build/lib/build/lib/build/lib/nabu/opencl/fft.py +0 -6
  1401. build/lib/build/lib/build/lib/nabu/opencl/kernel.py +0 -135
  1402. build/lib/build/lib/build/lib/nabu/opencl/memcpy.py +0 -35
  1403. build/lib/build/lib/build/lib/nabu/opencl/padding.py +0 -6
  1404. build/lib/build/lib/build/lib/nabu/opencl/processing.py +0 -62
  1405. build/lib/build/lib/build/lib/nabu/opencl/tests/__init__.py +0 -0
  1406. build/lib/build/lib/build/lib/nabu/opencl/utils.py +0 -292
  1407. build/lib/build/lib/build/lib/nabu/pipeline/__init__.py +0 -0
  1408. build/lib/build/lib/build/lib/nabu/pipeline/config.py +0 -265
  1409. build/lib/build/lib/build/lib/nabu/pipeline/config_validators.py +0 -589
  1410. build/lib/build/lib/build/lib/nabu/pipeline/datadump.py +0 -164
  1411. build/lib/build/lib/build/lib/nabu/pipeline/dataset_validator.py +0 -211
  1412. build/lib/build/lib/build/lib/nabu/pipeline/detector_distortion_provider.py +0 -20
  1413. build/lib/build/lib/build/lib/nabu/pipeline/estimators.py +0 -1012
  1414. build/lib/build/lib/build/lib/nabu/pipeline/fallback_utils.py +0 -149
  1415. build/lib/build/lib/build/lib/nabu/pipeline/fullfield/__init__.py +0 -0
  1416. build/lib/build/lib/build/lib/nabu/pipeline/fullfield/chunked.py +0 -849
  1417. build/lib/build/lib/build/lib/nabu/pipeline/fullfield/chunked_cuda.py +0 -152
  1418. build/lib/build/lib/build/lib/nabu/pipeline/fullfield/computations.py +0 -260
  1419. build/lib/build/lib/build/lib/nabu/pipeline/fullfield/dataset_validator.py +0 -63
  1420. build/lib/build/lib/build/lib/nabu/pipeline/fullfield/nabu_config.py +0 -590
  1421. build/lib/build/lib/build/lib/nabu/pipeline/fullfield/processconfig.py +0 -825
  1422. build/lib/build/lib/build/lib/nabu/pipeline/fullfield/reconstruction.py +0 -851
  1423. build/lib/build/lib/build/lib/nabu/pipeline/helical/__init__.py +0 -0
  1424. build/lib/build/lib/build/lib/nabu/pipeline/helical/dataset_validator.py +0 -19
  1425. build/lib/build/lib/build/lib/nabu/pipeline/helical/fbp.py +0 -147
  1426. build/lib/build/lib/build/lib/nabu/pipeline/helical/filtering.py +0 -246
  1427. build/lib/build/lib/build/lib/nabu/pipeline/helical/gridded_accumulator.py +0 -575
  1428. build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_chunked_regridded.py +0 -1670
  1429. build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_chunked_regridded_cuda.py +0 -119
  1430. build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_reconstruction.py +0 -598
  1431. build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_utils.py +0 -42
  1432. build/lib/build/lib/build/lib/nabu/pipeline/helical/nabu_config.py +0 -175
  1433. build/lib/build/lib/build/lib/nabu/pipeline/helical/processconfig.py +0 -62
  1434. build/lib/build/lib/build/lib/nabu/pipeline/helical/span_strategy.py +0 -483
  1435. build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/__init__.py +0 -0
  1436. build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/test_accumulator.py +0 -157
  1437. build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/test_pipeline_elements_full.py +0 -355
  1438. build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/test_strategy.py +0 -61
  1439. build/lib/build/lib/build/lib/nabu/pipeline/helical/utils.py +0 -51
  1440. build/lib/build/lib/build/lib/nabu/pipeline/helical/weight_balancer.py +0 -101
  1441. build/lib/build/lib/build/lib/nabu/pipeline/params.py +0 -163
  1442. build/lib/build/lib/build/lib/nabu/pipeline/processconfig.py +0 -210
  1443. build/lib/build/lib/build/lib/nabu/pipeline/tests/test_chunk_reader.py +0 -78
  1444. build/lib/build/lib/build/lib/nabu/pipeline/tests/test_estimators.py +0 -149
  1445. build/lib/build/lib/build/lib/nabu/pipeline/utils.py +0 -116
  1446. build/lib/build/lib/build/lib/nabu/pipeline/writer.py +0 -193
  1447. build/lib/build/lib/build/lib/nabu/pipeline/xrdct/__init__.py +0 -0
  1448. build/lib/build/lib/build/lib/nabu/preproc/__init__.py +0 -7
  1449. build/lib/build/lib/build/lib/nabu/preproc/alignment.py +0 -11
  1450. build/lib/build/lib/build/lib/nabu/preproc/ccd.py +0 -161
  1451. build/lib/build/lib/build/lib/nabu/preproc/ccd_cuda.py +0 -169
  1452. build/lib/build/lib/build/lib/nabu/preproc/ctf.py +0 -361
  1453. build/lib/build/lib/build/lib/nabu/preproc/ctf_cuda.py +0 -142
  1454. build/lib/build/lib/build/lib/nabu/preproc/distortion.py +0 -92
  1455. build/lib/build/lib/build/lib/nabu/preproc/double_flatfield.py +0 -212
  1456. build/lib/build/lib/build/lib/nabu/preproc/double_flatfield_cuda.py +0 -174
  1457. build/lib/build/lib/build/lib/nabu/preproc/double_flatfield_variable_region.py +0 -68
  1458. build/lib/build/lib/build/lib/nabu/preproc/flatfield.py +0 -448
  1459. build/lib/build/lib/build/lib/nabu/preproc/flatfield_cuda.py +0 -144
  1460. build/lib/build/lib/build/lib/nabu/preproc/flatfield_variable_region.py +0 -79
  1461. build/lib/build/lib/build/lib/nabu/preproc/phase.py +0 -425
  1462. build/lib/build/lib/build/lib/nabu/preproc/phase_cuda.py +0 -143
  1463. build/lib/build/lib/build/lib/nabu/preproc/shift.py +0 -95
  1464. build/lib/build/lib/build/lib/nabu/preproc/shift_cuda.py +0 -102
  1465. build/lib/build/lib/build/lib/nabu/preproc/tests/__init__.py +0 -1
  1466. build/lib/build/lib/build/lib/nabu/preproc/tests/test_ccd_corr.py +0 -59
  1467. build/lib/build/lib/build/lib/nabu/preproc/tests/test_ctf.py +0 -250
  1468. build/lib/build/lib/build/lib/nabu/preproc/tests/test_double_flatfield.py +0 -86
  1469. build/lib/build/lib/build/lib/nabu/preproc/tests/test_flatfield.py +0 -626
  1470. build/lib/build/lib/build/lib/nabu/preproc/tests/test_paganin.py +0 -67
  1471. build/lib/build/lib/build/lib/nabu/preproc/tests/test_vshift.py +0 -73
  1472. build/lib/build/lib/build/lib/nabu/processing/__init__.py +0 -0
  1473. build/lib/build/lib/build/lib/nabu/processing/convolution_cuda.py +0 -375
  1474. build/lib/build/lib/build/lib/nabu/processing/fft_base.py +0 -163
  1475. build/lib/build/lib/build/lib/nabu/processing/fft_cuda.py +0 -256
  1476. build/lib/build/lib/build/lib/nabu/processing/fft_opencl.py +0 -54
  1477. build/lib/build/lib/build/lib/nabu/processing/fftshift.py +0 -134
  1478. build/lib/build/lib/build/lib/nabu/processing/histogram.py +0 -286
  1479. build/lib/build/lib/build/lib/nabu/processing/histogram_cuda.py +0 -103
  1480. build/lib/build/lib/build/lib/nabu/processing/kernel_base.py +0 -126
  1481. build/lib/build/lib/build/lib/nabu/processing/medfilt_cuda.py +0 -159
  1482. build/lib/build/lib/build/lib/nabu/processing/muladd.py +0 -29
  1483. build/lib/build/lib/build/lib/nabu/processing/muladd_cuda.py +0 -68
  1484. build/lib/build/lib/build/lib/nabu/processing/padding_base.py +0 -71
  1485. build/lib/build/lib/build/lib/nabu/processing/padding_cuda.py +0 -75
  1486. build/lib/build/lib/build/lib/nabu/processing/padding_opencl.py +0 -77
  1487. build/lib/build/lib/build/lib/nabu/processing/processing_base.py +0 -123
  1488. build/lib/build/lib/build/lib/nabu/processing/roll_opencl.py +0 -64
  1489. build/lib/build/lib/build/lib/nabu/processing/rotation.py +0 -63
  1490. build/lib/build/lib/build/lib/nabu/processing/rotation_cuda.py +0 -66
  1491. build/lib/build/lib/build/lib/nabu/processing/tests/__init__.py +0 -0
  1492. build/lib/build/lib/build/lib/nabu/processing/tests/test_fft.py +0 -268
  1493. build/lib/build/lib/build/lib/nabu/processing/tests/test_fftshift.py +0 -71
  1494. build/lib/build/lib/build/lib/nabu/processing/tests/test_histogram.py +0 -55
  1495. build/lib/build/lib/build/lib/nabu/processing/tests/test_medfilt.py +0 -77
  1496. build/lib/build/lib/build/lib/nabu/processing/tests/test_muladd.py +0 -54
  1497. build/lib/build/lib/build/lib/nabu/processing/tests/test_padding.py +0 -247
  1498. build/lib/build/lib/build/lib/nabu/processing/tests/test_roll.py +0 -63
  1499. build/lib/build/lib/build/lib/nabu/processing/tests/test_rotation.py +0 -83
  1500. build/lib/build/lib/build/lib/nabu/processing/tests/test_transpose.py +0 -72
  1501. build/lib/build/lib/build/lib/nabu/processing/tests/test_unsharp.py +0 -106
  1502. build/lib/build/lib/build/lib/nabu/processing/transpose.py +0 -126
  1503. build/lib/build/lib/build/lib/nabu/processing/unsharp.py +0 -79
  1504. build/lib/build/lib/build/lib/nabu/processing/unsharp_cuda.py +0 -53
  1505. build/lib/build/lib/build/lib/nabu/processing/unsharp_opencl.py +0 -75
  1506. build/lib/build/lib/build/lib/nabu/reconstruction/__init__.py +0 -3
  1507. build/lib/build/lib/build/lib/nabu/reconstruction/cone.py +0 -241
  1508. build/lib/build/lib/build/lib/nabu/reconstruction/fbp.py +0 -124
  1509. build/lib/build/lib/build/lib/nabu/reconstruction/fbp_base.py +0 -391
  1510. build/lib/build/lib/build/lib/nabu/reconstruction/fbp_opencl.py +0 -78
  1511. build/lib/build/lib/build/lib/nabu/reconstruction/filtering.py +0 -220
  1512. build/lib/build/lib/build/lib/nabu/reconstruction/filtering_cuda.py +0 -103
  1513. build/lib/build/lib/build/lib/nabu/reconstruction/filtering_opencl.py +0 -111
  1514. build/lib/build/lib/build/lib/nabu/reconstruction/projection.py +0 -240
  1515. build/lib/build/lib/build/lib/nabu/reconstruction/reconstructor.py +0 -174
  1516. build/lib/build/lib/build/lib/nabu/reconstruction/reconstructor_cuda.py +0 -44
  1517. build/lib/build/lib/build/lib/nabu/reconstruction/rings.py +0 -248
  1518. build/lib/build/lib/build/lib/nabu/reconstruction/rings_cuda.py +0 -322
  1519. build/lib/build/lib/build/lib/nabu/reconstruction/sinogram.py +0 -467
  1520. build/lib/build/lib/build/lib/nabu/reconstruction/sinogram_cuda.py +0 -250
  1521. build/lib/build/lib/build/lib/nabu/reconstruction/sinogram_opencl.py +0 -40
  1522. build/lib/build/lib/build/lib/nabu/reconstruction/tests/__init__.py +0 -1
  1523. build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_cone.py +0 -308
  1524. build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_deringer.py +0 -220
  1525. build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_fbp.py +0 -252
  1526. build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_filtering.py +0 -133
  1527. build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_halftomo.py +0 -100
  1528. build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_projector.py +0 -164
  1529. build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_reconstructor.py +0 -93
  1530. build/lib/build/lib/build/lib/nabu/reconstruction/tests/test_sino_normalization.py +0 -85
  1531. build/lib/build/lib/build/lib/nabu/resources/__init__.py +0 -0
  1532. build/lib/build/lib/build/lib/nabu/resources/cli/__init__.py +0 -0
  1533. build/lib/build/lib/build/lib/nabu/resources/cor.py +0 -5
  1534. build/lib/build/lib/build/lib/nabu/resources/dataset_analyzer.py +0 -469
  1535. build/lib/build/lib/build/lib/nabu/resources/gpu.py +0 -169
  1536. build/lib/build/lib/build/lib/nabu/resources/logger.py +0 -130
  1537. build/lib/build/lib/build/lib/nabu/resources/nxflatfield.py +0 -217
  1538. build/lib/build/lib/build/lib/nabu/resources/templates/__init__.py +0 -0
  1539. build/lib/build/lib/build/lib/nabu/resources/tests/__init__.py +0 -0
  1540. build/lib/build/lib/build/lib/nabu/resources/tests/test_nxflatfield.py +0 -104
  1541. build/lib/build/lib/build/lib/nabu/resources/tests/test_units.py +0 -47
  1542. build/lib/build/lib/build/lib/nabu/resources/utils.py +0 -174
  1543. build/lib/build/lib/build/lib/nabu/stitching/__init__.py +0 -0
  1544. build/lib/build/lib/build/lib/nabu/stitching/alignment.py +0 -184
  1545. build/lib/build/lib/build/lib/nabu/stitching/config.py +0 -1286
  1546. build/lib/build/lib/build/lib/nabu/stitching/definitions.py +0 -6
  1547. build/lib/build/lib/build/lib/nabu/stitching/frame_composition.py +0 -155
  1548. build/lib/build/lib/build/lib/nabu/stitching/overlap.py +0 -373
  1549. build/lib/build/lib/build/lib/nabu/stitching/sample_normalization.py +0 -60
  1550. build/lib/build/lib/build/lib/nabu/stitching/slurm_utils.py +0 -204
  1551. build/lib/build/lib/build/lib/nabu/stitching/tests/__init__.py +0 -0
  1552. build/lib/build/lib/build/lib/nabu/stitching/tests/test_alignment.py +0 -99
  1553. build/lib/build/lib/build/lib/nabu/stitching/tests/test_config.py +0 -226
  1554. build/lib/build/lib/build/lib/nabu/stitching/tests/test_frame_composition.py +0 -180
  1555. build/lib/build/lib/build/lib/nabu/stitching/tests/test_overlap.py +0 -98
  1556. build/lib/build/lib/build/lib/nabu/stitching/tests/test_sample_normalization.py +0 -49
  1557. build/lib/build/lib/build/lib/nabu/stitching/tests/test_slurm_utils.py +0 -146
  1558. build/lib/build/lib/build/lib/nabu/stitching/tests/test_utils.py +0 -21
  1559. build/lib/build/lib/build/lib/nabu/stitching/tests/test_z_stitching.py +0 -1183
  1560. build/lib/build/lib/build/lib/nabu/stitching/utils.py +0 -563
  1561. build/lib/build/lib/build/lib/nabu/stitching/z_stitching.py +0 -2279
  1562. build/lib/build/lib/build/lib/nabu/tests.py +0 -51
  1563. build/lib/build/lib/build/lib/nabu/testutils.py +0 -375
  1564. build/lib/build/lib/build/lib/nabu/thirdparty/__init__.py +0 -0
  1565. build/lib/build/lib/build/lib/nabu/thirdparty/algotom_convert_sino.py +0 -276
  1566. build/lib/build/lib/build/lib/nabu/thirdparty/pore3d_deringer_munch.py +0 -108
  1567. build/lib/build/lib/build/lib/nabu/thirdparty/tomocupy_remove_stripe.py +0 -586
  1568. build/lib/build/lib/build/lib/nabu/thirdparty/tomopy_phase.py +0 -239
  1569. build/lib/build/lib/build/lib/nabu/thirdparty/tomwer_load_flats_darks.py +0 -162
  1570. build/lib/build/lib/build/lib/nabu/utils.py +0 -836
  1571. build/lib/build/lib/doc/conf.py +0 -137
  1572. build/lib/build/lib/doc/create_conf_doc.py +0 -38
  1573. build/lib/build/lib/doc/get_mathjax.py +0 -34
  1574. build/lib/build/lib/nabu/__init__.py +0 -17
  1575. build/lib/build/lib/nabu/app/__init__.py +0 -0
  1576. build/lib/build/lib/nabu/app/bootstrap.py +0 -88
  1577. build/lib/build/lib/nabu/app/bootstrap_stitching.py +0 -69
  1578. build/lib/build/lib/nabu/app/cast_volume.py +0 -272
  1579. build/lib/build/lib/nabu/app/cli_configs.py +0 -626
  1580. build/lib/build/lib/nabu/app/compare_volumes.py +0 -94
  1581. build/lib/build/lib/nabu/app/composite_cor.py +0 -144
  1582. build/lib/build/lib/nabu/app/correct_rot.py +0 -70
  1583. build/lib/build/lib/nabu/app/create_distortion_map_from_poly.py +0 -153
  1584. build/lib/build/lib/nabu/app/diag_to_pix.py +0 -358
  1585. build/lib/build/lib/nabu/app/diag_to_rot.py +0 -449
  1586. build/lib/build/lib/nabu/app/double_flatfield.py +0 -143
  1587. build/lib/build/lib/nabu/app/generate_header.py +0 -261
  1588. build/lib/build/lib/nabu/app/histogram.py +0 -197
  1589. build/lib/build/lib/nabu/app/multicor.py +0 -90
  1590. build/lib/build/lib/nabu/app/nx_z_splitter.py +0 -125
  1591. build/lib/build/lib/nabu/app/parse_reconstruction_log.py +0 -151
  1592. build/lib/build/lib/nabu/app/prepare_weights_double.py +0 -163
  1593. build/lib/build/lib/nabu/app/reconstruct.py +0 -120
  1594. build/lib/build/lib/nabu/app/reconstruct_helical.py +0 -116
  1595. build/lib/build/lib/nabu/app/reduce_dark_flat.py +0 -181
  1596. build/lib/build/lib/nabu/app/rotate.py +0 -162
  1597. build/lib/build/lib/nabu/app/shrink_dataset.py +0 -98
  1598. build/lib/build/lib/nabu/app/stitching.py +0 -85
  1599. build/lib/build/lib/nabu/app/tests/test_reduce_dark_flat.py +0 -78
  1600. build/lib/build/lib/nabu/app/utils.py +0 -33
  1601. build/lib/build/lib/nabu/app/validator.py +0 -110
  1602. build/lib/build/lib/nabu/cuda/__init__.py +0 -0
  1603. build/lib/build/lib/nabu/cuda/convolution.py +0 -8
  1604. build/lib/build/lib/nabu/cuda/fft.py +0 -4
  1605. build/lib/build/lib/nabu/cuda/kernel.py +0 -97
  1606. build/lib/build/lib/nabu/cuda/medfilt.py +0 -6
  1607. build/lib/build/lib/nabu/cuda/padding.py +0 -6
  1608. build/lib/build/lib/nabu/cuda/processing.py +0 -75
  1609. build/lib/build/lib/nabu/cuda/tests/__init__.py +0 -1
  1610. build/lib/build/lib/nabu/cuda/utils.py +0 -331
  1611. build/lib/build/lib/nabu/estimation/__init__.py +0 -12
  1612. build/lib/build/lib/nabu/estimation/alignment.py +0 -578
  1613. build/lib/build/lib/nabu/estimation/cor.py +0 -1621
  1614. build/lib/build/lib/nabu/estimation/cor_sino.py +0 -183
  1615. build/lib/build/lib/nabu/estimation/distortion.py +0 -112
  1616. build/lib/build/lib/nabu/estimation/focus.py +0 -362
  1617. build/lib/build/lib/nabu/estimation/tests/__init__.py +0 -0
  1618. build/lib/build/lib/nabu/estimation/tests/test_alignment.py +0 -70
  1619. build/lib/build/lib/nabu/estimation/tests/test_cor.py +0 -472
  1620. build/lib/build/lib/nabu/estimation/tests/test_focus.py +0 -105
  1621. build/lib/build/lib/nabu/estimation/tests/test_tilt.py +0 -41
  1622. build/lib/build/lib/nabu/estimation/tests/test_translation.py +0 -78
  1623. build/lib/build/lib/nabu/estimation/tilt.py +0 -214
  1624. build/lib/build/lib/nabu/estimation/translation.py +0 -193
  1625. build/lib/build/lib/nabu/estimation/utils.py +0 -39
  1626. build/lib/build/lib/nabu/io/__init__.py +0 -2
  1627. build/lib/build/lib/nabu/io/cast_volume.py +0 -371
  1628. build/lib/build/lib/nabu/io/detector_distortion.py +0 -305
  1629. build/lib/build/lib/nabu/io/reader.py +0 -628
  1630. build/lib/build/lib/nabu/io/reader_helical.py +0 -114
  1631. build/lib/build/lib/nabu/io/tests/__init__.py +0 -0
  1632. build/lib/build/lib/nabu/io/tests/test_cast_volume.py +0 -339
  1633. build/lib/build/lib/nabu/io/tests/test_detector_distortion.py +0 -178
  1634. build/lib/build/lib/nabu/io/tests/test_writers.py +0 -187
  1635. build/lib/build/lib/nabu/io/tiffwriter_zmm.py +0 -99
  1636. build/lib/build/lib/nabu/io/utils.py +0 -263
  1637. build/lib/build/lib/nabu/io/writer.py +0 -892
  1638. build/lib/build/lib/nabu/misc/__init__.py +0 -0
  1639. build/lib/build/lib/nabu/misc/binning.py +0 -98
  1640. build/lib/build/lib/nabu/misc/fftshift.py +0 -6
  1641. build/lib/build/lib/nabu/misc/filters.py +0 -24
  1642. build/lib/build/lib/nabu/misc/fourier_filters.py +0 -152
  1643. build/lib/build/lib/nabu/misc/histogram.py +0 -6
  1644. build/lib/build/lib/nabu/misc/histogram_cuda.py +0 -8
  1645. build/lib/build/lib/nabu/misc/kernel_base.py +0 -4
  1646. build/lib/build/lib/nabu/misc/padding.py +0 -83
  1647. build/lib/build/lib/nabu/misc/padding_base.py +0 -6
  1648. build/lib/build/lib/nabu/misc/processing_base.py +0 -4
  1649. build/lib/build/lib/nabu/misc/rotation.py +0 -6
  1650. build/lib/build/lib/nabu/misc/rotation_cuda.py +0 -6
  1651. build/lib/build/lib/nabu/misc/tests/__init__.py +0 -1
  1652. build/lib/build/lib/nabu/misc/tests/test_binning.py +0 -48
  1653. build/lib/build/lib/nabu/misc/tests/test_interpolation.py +0 -70
  1654. build/lib/build/lib/nabu/misc/transpose.py +0 -6
  1655. build/lib/build/lib/nabu/misc/unsharp.py +0 -4
  1656. build/lib/build/lib/nabu/misc/unsharp_cuda.py +0 -6
  1657. build/lib/build/lib/nabu/misc/unsharp_opencl.py +0 -8
  1658. build/lib/build/lib/nabu/misc/utils.py +0 -117
  1659. build/lib/build/lib/nabu/opencl/__init__.py +0 -0
  1660. build/lib/build/lib/nabu/opencl/fft.py +0 -6
  1661. build/lib/build/lib/nabu/opencl/kernel.py +0 -135
  1662. build/lib/build/lib/nabu/opencl/memcpy.py +0 -35
  1663. build/lib/build/lib/nabu/opencl/padding.py +0 -6
  1664. build/lib/build/lib/nabu/opencl/processing.py +0 -62
  1665. build/lib/build/lib/nabu/opencl/tests/__init__.py +0 -0
  1666. build/lib/build/lib/nabu/opencl/utils.py +0 -292
  1667. build/lib/build/lib/nabu/pipeline/__init__.py +0 -0
  1668. build/lib/build/lib/nabu/pipeline/config.py +0 -265
  1669. build/lib/build/lib/nabu/pipeline/config_validators.py +0 -589
  1670. build/lib/build/lib/nabu/pipeline/datadump.py +0 -164
  1671. build/lib/build/lib/nabu/pipeline/dataset_validator.py +0 -211
  1672. build/lib/build/lib/nabu/pipeline/detector_distortion_provider.py +0 -20
  1673. build/lib/build/lib/nabu/pipeline/estimators.py +0 -1012
  1674. build/lib/build/lib/nabu/pipeline/fallback_utils.py +0 -149
  1675. build/lib/build/lib/nabu/pipeline/fullfield/__init__.py +0 -0
  1676. build/lib/build/lib/nabu/pipeline/fullfield/chunked.py +0 -849
  1677. build/lib/build/lib/nabu/pipeline/fullfield/chunked_cuda.py +0 -152
  1678. build/lib/build/lib/nabu/pipeline/fullfield/computations.py +0 -260
  1679. build/lib/build/lib/nabu/pipeline/fullfield/dataset_validator.py +0 -63
  1680. build/lib/build/lib/nabu/pipeline/fullfield/nabu_config.py +0 -590
  1681. build/lib/build/lib/nabu/pipeline/fullfield/processconfig.py +0 -825
  1682. build/lib/build/lib/nabu/pipeline/fullfield/reconstruction.py +0 -851
  1683. build/lib/build/lib/nabu/pipeline/helical/__init__.py +0 -0
  1684. build/lib/build/lib/nabu/pipeline/helical/dataset_validator.py +0 -19
  1685. build/lib/build/lib/nabu/pipeline/helical/fbp.py +0 -147
  1686. build/lib/build/lib/nabu/pipeline/helical/filtering.py +0 -246
  1687. build/lib/build/lib/nabu/pipeline/helical/gridded_accumulator.py +0 -575
  1688. build/lib/build/lib/nabu/pipeline/helical/helical_chunked_regridded.py +0 -1670
  1689. build/lib/build/lib/nabu/pipeline/helical/helical_chunked_regridded_cuda.py +0 -119
  1690. build/lib/build/lib/nabu/pipeline/helical/helical_reconstruction.py +0 -598
  1691. build/lib/build/lib/nabu/pipeline/helical/helical_utils.py +0 -42
  1692. build/lib/build/lib/nabu/pipeline/helical/nabu_config.py +0 -175
  1693. build/lib/build/lib/nabu/pipeline/helical/processconfig.py +0 -62
  1694. build/lib/build/lib/nabu/pipeline/helical/span_strategy.py +0 -483
  1695. build/lib/build/lib/nabu/pipeline/helical/tests/__init__.py +0 -0
  1696. build/lib/build/lib/nabu/pipeline/helical/tests/test_accumulator.py +0 -157
  1697. build/lib/build/lib/nabu/pipeline/helical/tests/test_pipeline_elements_full.py +0 -355
  1698. build/lib/build/lib/nabu/pipeline/helical/tests/test_strategy.py +0 -61
  1699. build/lib/build/lib/nabu/pipeline/helical/utils.py +0 -51
  1700. build/lib/build/lib/nabu/pipeline/helical/weight_balancer.py +0 -101
  1701. build/lib/build/lib/nabu/pipeline/params.py +0 -163
  1702. build/lib/build/lib/nabu/pipeline/processconfig.py +0 -210
  1703. build/lib/build/lib/nabu/pipeline/tests/test_chunk_reader.py +0 -78
  1704. build/lib/build/lib/nabu/pipeline/tests/test_estimators.py +0 -149
  1705. build/lib/build/lib/nabu/pipeline/utils.py +0 -116
  1706. build/lib/build/lib/nabu/pipeline/writer.py +0 -193
  1707. build/lib/build/lib/nabu/pipeline/xrdct/__init__.py +0 -0
  1708. build/lib/build/lib/nabu/preproc/__init__.py +0 -7
  1709. build/lib/build/lib/nabu/preproc/alignment.py +0 -11
  1710. build/lib/build/lib/nabu/preproc/ccd.py +0 -161
  1711. build/lib/build/lib/nabu/preproc/ccd_cuda.py +0 -169
  1712. build/lib/build/lib/nabu/preproc/ctf.py +0 -361
  1713. build/lib/build/lib/nabu/preproc/ctf_cuda.py +0 -142
  1714. build/lib/build/lib/nabu/preproc/distortion.py +0 -92
  1715. build/lib/build/lib/nabu/preproc/double_flatfield.py +0 -212
  1716. build/lib/build/lib/nabu/preproc/double_flatfield_cuda.py +0 -174
  1717. build/lib/build/lib/nabu/preproc/double_flatfield_variable_region.py +0 -68
  1718. build/lib/build/lib/nabu/preproc/flatfield.py +0 -448
  1719. build/lib/build/lib/nabu/preproc/flatfield_cuda.py +0 -144
  1720. build/lib/build/lib/nabu/preproc/flatfield_variable_region.py +0 -79
  1721. build/lib/build/lib/nabu/preproc/phase.py +0 -425
  1722. build/lib/build/lib/nabu/preproc/phase_cuda.py +0 -143
  1723. build/lib/build/lib/nabu/preproc/shift.py +0 -95
  1724. build/lib/build/lib/nabu/preproc/shift_cuda.py +0 -102
  1725. build/lib/build/lib/nabu/preproc/tests/__init__.py +0 -1
  1726. build/lib/build/lib/nabu/preproc/tests/test_ccd_corr.py +0 -59
  1727. build/lib/build/lib/nabu/preproc/tests/test_ctf.py +0 -250
  1728. build/lib/build/lib/nabu/preproc/tests/test_double_flatfield.py +0 -86
  1729. build/lib/build/lib/nabu/preproc/tests/test_flatfield.py +0 -626
  1730. build/lib/build/lib/nabu/preproc/tests/test_paganin.py +0 -67
  1731. build/lib/build/lib/nabu/preproc/tests/test_vshift.py +0 -73
  1732. build/lib/build/lib/nabu/processing/__init__.py +0 -0
  1733. build/lib/build/lib/nabu/processing/convolution_cuda.py +0 -375
  1734. build/lib/build/lib/nabu/processing/fft_base.py +0 -163
  1735. build/lib/build/lib/nabu/processing/fft_cuda.py +0 -256
  1736. build/lib/build/lib/nabu/processing/fft_opencl.py +0 -54
  1737. build/lib/build/lib/nabu/processing/fftshift.py +0 -134
  1738. build/lib/build/lib/nabu/processing/histogram.py +0 -286
  1739. build/lib/build/lib/nabu/processing/histogram_cuda.py +0 -103
  1740. build/lib/build/lib/nabu/processing/kernel_base.py +0 -126
  1741. build/lib/build/lib/nabu/processing/medfilt_cuda.py +0 -159
  1742. build/lib/build/lib/nabu/processing/muladd.py +0 -29
  1743. build/lib/build/lib/nabu/processing/muladd_cuda.py +0 -68
  1744. build/lib/build/lib/nabu/processing/padding_base.py +0 -71
  1745. build/lib/build/lib/nabu/processing/padding_cuda.py +0 -75
  1746. build/lib/build/lib/nabu/processing/padding_opencl.py +0 -77
  1747. build/lib/build/lib/nabu/processing/processing_base.py +0 -123
  1748. build/lib/build/lib/nabu/processing/roll_opencl.py +0 -64
  1749. build/lib/build/lib/nabu/processing/rotation.py +0 -63
  1750. build/lib/build/lib/nabu/processing/rotation_cuda.py +0 -66
  1751. build/lib/build/lib/nabu/processing/tests/__init__.py +0 -0
  1752. build/lib/build/lib/nabu/processing/tests/test_fft.py +0 -268
  1753. build/lib/build/lib/nabu/processing/tests/test_fftshift.py +0 -71
  1754. build/lib/build/lib/nabu/processing/tests/test_histogram.py +0 -55
  1755. build/lib/build/lib/nabu/processing/tests/test_medfilt.py +0 -77
  1756. build/lib/build/lib/nabu/processing/tests/test_muladd.py +0 -54
  1757. build/lib/build/lib/nabu/processing/tests/test_padding.py +0 -247
  1758. build/lib/build/lib/nabu/processing/tests/test_roll.py +0 -63
  1759. build/lib/build/lib/nabu/processing/tests/test_rotation.py +0 -83
  1760. build/lib/build/lib/nabu/processing/tests/test_transpose.py +0 -72
  1761. build/lib/build/lib/nabu/processing/tests/test_unsharp.py +0 -106
  1762. build/lib/build/lib/nabu/processing/transpose.py +0 -126
  1763. build/lib/build/lib/nabu/processing/unsharp.py +0 -79
  1764. build/lib/build/lib/nabu/processing/unsharp_cuda.py +0 -53
  1765. build/lib/build/lib/nabu/processing/unsharp_opencl.py +0 -75
  1766. build/lib/build/lib/nabu/reconstruction/__init__.py +0 -3
  1767. build/lib/build/lib/nabu/reconstruction/cone.py +0 -241
  1768. build/lib/build/lib/nabu/reconstruction/fbp.py +0 -124
  1769. build/lib/build/lib/nabu/reconstruction/fbp_base.py +0 -391
  1770. build/lib/build/lib/nabu/reconstruction/fbp_opencl.py +0 -78
  1771. build/lib/build/lib/nabu/reconstruction/filtering.py +0 -220
  1772. build/lib/build/lib/nabu/reconstruction/filtering_cuda.py +0 -103
  1773. build/lib/build/lib/nabu/reconstruction/filtering_opencl.py +0 -111
  1774. build/lib/build/lib/nabu/reconstruction/projection.py +0 -240
  1775. build/lib/build/lib/nabu/reconstruction/reconstructor.py +0 -174
  1776. build/lib/build/lib/nabu/reconstruction/reconstructor_cuda.py +0 -44
  1777. build/lib/build/lib/nabu/reconstruction/rings.py +0 -248
  1778. build/lib/build/lib/nabu/reconstruction/rings_cuda.py +0 -322
  1779. build/lib/build/lib/nabu/reconstruction/sinogram.py +0 -467
  1780. build/lib/build/lib/nabu/reconstruction/sinogram_cuda.py +0 -250
  1781. build/lib/build/lib/nabu/reconstruction/sinogram_opencl.py +0 -40
  1782. build/lib/build/lib/nabu/reconstruction/tests/__init__.py +0 -1
  1783. build/lib/build/lib/nabu/reconstruction/tests/test_cone.py +0 -308
  1784. build/lib/build/lib/nabu/reconstruction/tests/test_deringer.py +0 -220
  1785. build/lib/build/lib/nabu/reconstruction/tests/test_fbp.py +0 -252
  1786. build/lib/build/lib/nabu/reconstruction/tests/test_filtering.py +0 -133
  1787. build/lib/build/lib/nabu/reconstruction/tests/test_halftomo.py +0 -100
  1788. build/lib/build/lib/nabu/reconstruction/tests/test_projector.py +0 -164
  1789. build/lib/build/lib/nabu/reconstruction/tests/test_reconstructor.py +0 -93
  1790. build/lib/build/lib/nabu/reconstruction/tests/test_sino_normalization.py +0 -85
  1791. build/lib/build/lib/nabu/resources/__init__.py +0 -0
  1792. build/lib/build/lib/nabu/resources/cli/__init__.py +0 -0
  1793. build/lib/build/lib/nabu/resources/cor.py +0 -5
  1794. build/lib/build/lib/nabu/resources/dataset_analyzer.py +0 -469
  1795. build/lib/build/lib/nabu/resources/gpu.py +0 -169
  1796. build/lib/build/lib/nabu/resources/logger.py +0 -130
  1797. build/lib/build/lib/nabu/resources/nxflatfield.py +0 -217
  1798. build/lib/build/lib/nabu/resources/templates/__init__.py +0 -0
  1799. build/lib/build/lib/nabu/resources/tests/__init__.py +0 -0
  1800. build/lib/build/lib/nabu/resources/tests/test_nxflatfield.py +0 -104
  1801. build/lib/build/lib/nabu/resources/tests/test_units.py +0 -47
  1802. build/lib/build/lib/nabu/resources/utils.py +0 -174
  1803. build/lib/build/lib/nabu/stitching/__init__.py +0 -0
  1804. build/lib/build/lib/nabu/stitching/alignment.py +0 -184
  1805. build/lib/build/lib/nabu/stitching/config.py +0 -1286
  1806. build/lib/build/lib/nabu/stitching/definitions.py +0 -6
  1807. build/lib/build/lib/nabu/stitching/frame_composition.py +0 -155
  1808. build/lib/build/lib/nabu/stitching/overlap.py +0 -373
  1809. build/lib/build/lib/nabu/stitching/sample_normalization.py +0 -60
  1810. build/lib/build/lib/nabu/stitching/slurm_utils.py +0 -204
  1811. build/lib/build/lib/nabu/stitching/tests/__init__.py +0 -0
  1812. build/lib/build/lib/nabu/stitching/tests/test_alignment.py +0 -99
  1813. build/lib/build/lib/nabu/stitching/tests/test_config.py +0 -226
  1814. build/lib/build/lib/nabu/stitching/tests/test_frame_composition.py +0 -180
  1815. build/lib/build/lib/nabu/stitching/tests/test_overlap.py +0 -98
  1816. build/lib/build/lib/nabu/stitching/tests/test_sample_normalization.py +0 -49
  1817. build/lib/build/lib/nabu/stitching/tests/test_slurm_utils.py +0 -146
  1818. build/lib/build/lib/nabu/stitching/tests/test_utils.py +0 -21
  1819. build/lib/build/lib/nabu/stitching/tests/test_z_stitching.py +0 -1183
  1820. build/lib/build/lib/nabu/stitching/utils.py +0 -563
  1821. build/lib/build/lib/nabu/stitching/z_stitching.py +0 -2279
  1822. build/lib/build/lib/nabu/tests.py +0 -51
  1823. build/lib/build/lib/nabu/testutils.py +0 -375
  1824. build/lib/build/lib/nabu/thirdparty/__init__.py +0 -0
  1825. build/lib/build/lib/nabu/thirdparty/algotom_convert_sino.py +0 -276
  1826. build/lib/build/lib/nabu/thirdparty/pore3d_deringer_munch.py +0 -108
  1827. build/lib/build/lib/nabu/thirdparty/tomocupy_remove_stripe.py +0 -586
  1828. build/lib/build/lib/nabu/thirdparty/tomopy_phase.py +0 -239
  1829. build/lib/build/lib/nabu/thirdparty/tomwer_load_flats_darks.py +0 -162
  1830. build/lib/build/lib/nabu/utils.py +0 -836
  1831. build/lib/doc/conf.py +0 -137
  1832. build/lib/doc/create_conf_doc.py +0 -38
  1833. build/lib/doc/get_mathjax.py +0 -34
  1834. build/lib/nabu/__init__.py +0 -17
  1835. build/lib/nabu/app/__init__.py +0 -0
  1836. build/lib/nabu/app/bootstrap.py +0 -88
  1837. build/lib/nabu/app/bootstrap_stitching.py +0 -69
  1838. build/lib/nabu/app/cast_volume.py +0 -272
  1839. build/lib/nabu/app/cli_configs.py +0 -626
  1840. build/lib/nabu/app/compare_volumes.py +0 -94
  1841. build/lib/nabu/app/composite_cor.py +0 -144
  1842. build/lib/nabu/app/correct_rot.py +0 -70
  1843. build/lib/nabu/app/create_distortion_map_from_poly.py +0 -153
  1844. build/lib/nabu/app/diag_to_pix.py +0 -358
  1845. build/lib/nabu/app/diag_to_rot.py +0 -449
  1846. build/lib/nabu/app/double_flatfield.py +0 -143
  1847. build/lib/nabu/app/generate_header.py +0 -261
  1848. build/lib/nabu/app/histogram.py +0 -197
  1849. build/lib/nabu/app/multicor.py +0 -90
  1850. build/lib/nabu/app/nx_z_splitter.py +0 -125
  1851. build/lib/nabu/app/parse_reconstruction_log.py +0 -151
  1852. build/lib/nabu/app/prepare_weights_double.py +0 -163
  1853. build/lib/nabu/app/reconstruct.py +0 -120
  1854. build/lib/nabu/app/reconstruct_helical.py +0 -116
  1855. build/lib/nabu/app/reduce_dark_flat.py +0 -181
  1856. build/lib/nabu/app/rotate.py +0 -162
  1857. build/lib/nabu/app/shrink_dataset.py +0 -98
  1858. build/lib/nabu/app/stitching.py +0 -85
  1859. build/lib/nabu/app/tests/test_reduce_dark_flat.py +0 -78
  1860. build/lib/nabu/app/utils.py +0 -33
  1861. build/lib/nabu/app/validator.py +0 -110
  1862. build/lib/nabu/cuda/__init__.py +0 -0
  1863. build/lib/nabu/cuda/convolution.py +0 -8
  1864. build/lib/nabu/cuda/fft.py +0 -4
  1865. build/lib/nabu/cuda/kernel.py +0 -97
  1866. build/lib/nabu/cuda/medfilt.py +0 -6
  1867. build/lib/nabu/cuda/padding.py +0 -6
  1868. build/lib/nabu/cuda/processing.py +0 -75
  1869. build/lib/nabu/cuda/tests/__init__.py +0 -1
  1870. build/lib/nabu/cuda/utils.py +0 -331
  1871. build/lib/nabu/estimation/__init__.py +0 -12
  1872. build/lib/nabu/estimation/alignment.py +0 -578
  1873. build/lib/nabu/estimation/cor.py +0 -1621
  1874. build/lib/nabu/estimation/cor_sino.py +0 -183
  1875. build/lib/nabu/estimation/distortion.py +0 -112
  1876. build/lib/nabu/estimation/focus.py +0 -362
  1877. build/lib/nabu/estimation/tests/__init__.py +0 -0
  1878. build/lib/nabu/estimation/tests/test_alignment.py +0 -70
  1879. build/lib/nabu/estimation/tests/test_cor.py +0 -472
  1880. build/lib/nabu/estimation/tests/test_focus.py +0 -105
  1881. build/lib/nabu/estimation/tests/test_tilt.py +0 -41
  1882. build/lib/nabu/estimation/tests/test_translation.py +0 -78
  1883. build/lib/nabu/estimation/tilt.py +0 -214
  1884. build/lib/nabu/estimation/translation.py +0 -193
  1885. build/lib/nabu/estimation/utils.py +0 -39
  1886. build/lib/nabu/io/__init__.py +0 -2
  1887. build/lib/nabu/io/cast_volume.py +0 -371
  1888. build/lib/nabu/io/detector_distortion.py +0 -305
  1889. build/lib/nabu/io/reader.py +0 -628
  1890. build/lib/nabu/io/reader_helical.py +0 -114
  1891. build/lib/nabu/io/tests/__init__.py +0 -0
  1892. build/lib/nabu/io/tests/test_cast_volume.py +0 -339
  1893. build/lib/nabu/io/tests/test_detector_distortion.py +0 -178
  1894. build/lib/nabu/io/tests/test_writers.py +0 -187
  1895. build/lib/nabu/io/tiffwriter_zmm.py +0 -99
  1896. build/lib/nabu/io/utils.py +0 -263
  1897. build/lib/nabu/io/writer.py +0 -892
  1898. build/lib/nabu/misc/__init__.py +0 -0
  1899. build/lib/nabu/misc/binning.py +0 -98
  1900. build/lib/nabu/misc/fftshift.py +0 -6
  1901. build/lib/nabu/misc/filters.py +0 -24
  1902. build/lib/nabu/misc/fourier_filters.py +0 -152
  1903. build/lib/nabu/misc/histogram.py +0 -6
  1904. build/lib/nabu/misc/histogram_cuda.py +0 -8
  1905. build/lib/nabu/misc/kernel_base.py +0 -4
  1906. build/lib/nabu/misc/padding.py +0 -83
  1907. build/lib/nabu/misc/padding_base.py +0 -6
  1908. build/lib/nabu/misc/processing_base.py +0 -4
  1909. build/lib/nabu/misc/rotation.py +0 -6
  1910. build/lib/nabu/misc/rotation_cuda.py +0 -6
  1911. build/lib/nabu/misc/tests/__init__.py +0 -1
  1912. build/lib/nabu/misc/tests/test_binning.py +0 -48
  1913. build/lib/nabu/misc/tests/test_interpolation.py +0 -70
  1914. build/lib/nabu/misc/transpose.py +0 -6
  1915. build/lib/nabu/misc/unsharp.py +0 -4
  1916. build/lib/nabu/misc/unsharp_cuda.py +0 -6
  1917. build/lib/nabu/misc/unsharp_opencl.py +0 -8
  1918. build/lib/nabu/misc/utils.py +0 -117
  1919. build/lib/nabu/opencl/__init__.py +0 -0
  1920. build/lib/nabu/opencl/fft.py +0 -6
  1921. build/lib/nabu/opencl/kernel.py +0 -135
  1922. build/lib/nabu/opencl/memcpy.py +0 -35
  1923. build/lib/nabu/opencl/padding.py +0 -6
  1924. build/lib/nabu/opencl/processing.py +0 -62
  1925. build/lib/nabu/opencl/tests/__init__.py +0 -0
  1926. build/lib/nabu/opencl/utils.py +0 -292
  1927. build/lib/nabu/pipeline/__init__.py +0 -0
  1928. build/lib/nabu/pipeline/config.py +0 -265
  1929. build/lib/nabu/pipeline/config_validators.py +0 -589
  1930. build/lib/nabu/pipeline/datadump.py +0 -164
  1931. build/lib/nabu/pipeline/dataset_validator.py +0 -211
  1932. build/lib/nabu/pipeline/detector_distortion_provider.py +0 -20
  1933. build/lib/nabu/pipeline/estimators.py +0 -1012
  1934. build/lib/nabu/pipeline/fallback_utils.py +0 -149
  1935. build/lib/nabu/pipeline/fullfield/__init__.py +0 -0
  1936. build/lib/nabu/pipeline/fullfield/chunked.py +0 -849
  1937. build/lib/nabu/pipeline/fullfield/chunked_cuda.py +0 -152
  1938. build/lib/nabu/pipeline/fullfield/computations.py +0 -260
  1939. build/lib/nabu/pipeline/fullfield/dataset_validator.py +0 -63
  1940. build/lib/nabu/pipeline/fullfield/nabu_config.py +0 -590
  1941. build/lib/nabu/pipeline/fullfield/processconfig.py +0 -825
  1942. build/lib/nabu/pipeline/fullfield/reconstruction.py +0 -851
  1943. build/lib/nabu/pipeline/helical/__init__.py +0 -0
  1944. build/lib/nabu/pipeline/helical/dataset_validator.py +0 -19
  1945. build/lib/nabu/pipeline/helical/fbp.py +0 -147
  1946. build/lib/nabu/pipeline/helical/filtering.py +0 -246
  1947. build/lib/nabu/pipeline/helical/gridded_accumulator.py +0 -575
  1948. build/lib/nabu/pipeline/helical/helical_chunked_regridded.py +0 -1670
  1949. build/lib/nabu/pipeline/helical/helical_chunked_regridded_cuda.py +0 -119
  1950. build/lib/nabu/pipeline/helical/helical_reconstruction.py +0 -598
  1951. build/lib/nabu/pipeline/helical/helical_utils.py +0 -42
  1952. build/lib/nabu/pipeline/helical/nabu_config.py +0 -175
  1953. build/lib/nabu/pipeline/helical/processconfig.py +0 -62
  1954. build/lib/nabu/pipeline/helical/span_strategy.py +0 -483
  1955. build/lib/nabu/pipeline/helical/tests/__init__.py +0 -0
  1956. build/lib/nabu/pipeline/helical/tests/test_accumulator.py +0 -157
  1957. build/lib/nabu/pipeline/helical/tests/test_pipeline_elements_full.py +0 -355
  1958. build/lib/nabu/pipeline/helical/tests/test_strategy.py +0 -61
  1959. build/lib/nabu/pipeline/helical/utils.py +0 -51
  1960. build/lib/nabu/pipeline/helical/weight_balancer.py +0 -101
  1961. build/lib/nabu/pipeline/params.py +0 -163
  1962. build/lib/nabu/pipeline/processconfig.py +0 -210
  1963. build/lib/nabu/pipeline/tests/test_chunk_reader.py +0 -78
  1964. build/lib/nabu/pipeline/tests/test_estimators.py +0 -149
  1965. build/lib/nabu/pipeline/utils.py +0 -116
  1966. build/lib/nabu/pipeline/writer.py +0 -193
  1967. build/lib/nabu/pipeline/xrdct/__init__.py +0 -0
  1968. build/lib/nabu/preproc/__init__.py +0 -7
  1969. build/lib/nabu/preproc/alignment.py +0 -11
  1970. build/lib/nabu/preproc/ccd.py +0 -161
  1971. build/lib/nabu/preproc/ccd_cuda.py +0 -169
  1972. build/lib/nabu/preproc/ctf.py +0 -361
  1973. build/lib/nabu/preproc/ctf_cuda.py +0 -142
  1974. build/lib/nabu/preproc/distortion.py +0 -92
  1975. build/lib/nabu/preproc/double_flatfield.py +0 -212
  1976. build/lib/nabu/preproc/double_flatfield_cuda.py +0 -174
  1977. build/lib/nabu/preproc/double_flatfield_variable_region.py +0 -68
  1978. build/lib/nabu/preproc/flatfield.py +0 -448
  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
@@ -1,448 +0,0 @@
1
- from multiprocessing.pool import ThreadPool
2
- from bisect import bisect_left
3
- import numpy as np
4
- from ..io.reader import load_images_from_dataurl_dict
5
- from ..utils import check_supported, get_num_threads
6
-
7
-
8
- class FlatFieldArrays:
9
- """
10
- A class for flat-field normalization
11
- """
12
-
13
- # the variable below will be True for the derived class
14
- # which is taylored for to helical case
15
- _full_shape = False
16
-
17
- _supported_interpolations = ["linear", "nearest"]
18
-
19
- def __init__(
20
- self,
21
- radios_shape: tuple,
22
- flats,
23
- darks,
24
- radios_indices=None,
25
- interpolation: str = "linear",
26
- distortion_correction=None,
27
- nan_value=1.0,
28
- radios_srcurrent=None,
29
- flats_srcurrent=None,
30
- n_threads=None,
31
- ):
32
- """
33
- Initialize a flat-field normalization process.
34
-
35
- Parameters
36
- ----------
37
- radios_shape: tuple
38
- A tuple describing the shape of the radios stack, in the form
39
- `(n_radios, n_z, n_x)`.
40
- flats: dict
41
- Dictionary where each key is the flat index, and the value is a
42
- numpy.ndarray of the flat image.
43
- darks: dict
44
- Dictionary where each key is the dark index, and the value is a
45
- numpy.ndarray of the dark image.
46
- radios_indices: array of int, optional
47
- Array containing the radios indices in the scan. `radios_indices[0]` is the index
48
- of the first radio, and so on.
49
- interpolation: str, optional
50
- Interpolation method for flat-field. See below for more details.
51
- distortion_correction: DistortionCorrection, optional
52
- A DistortionCorrection object. If provided, it is used to correct flat distortions based on each radio.
53
- nan_value: float, optional
54
- Which float value is used to replace nan/inf after flat-field.
55
- radios_srcurrent: array, optional
56
- Array with the same shape as radios_indices. Each item contains the synchrotron electric current.
57
- If not None, normalization with current is applied.
58
- Please refer to "Notes" for more information on this normalization.
59
- flats_srcurrent: array, optional
60
- Array with the same length as "flats". Each item is a measurement of the synchrotron electric current
61
- for the corresponding flat. The items must be ordered in the same order as the flats indices (`flats.keys()`).
62
- This parameter must be used along with 'radios_srcurrent'.
63
- Please refer to "Notes" for more information on this normalization.
64
- n_threads: int or None, optional
65
- Number of threads to use for flat-field correction. Default is to use half the threads.
66
-
67
- Important
68
- ----------
69
- `flats` and `darks` are expected to be a dictionary with integer keys (the flats/darks indices)
70
- and numpy array values.
71
- You can use the following helper functions: `nabu.io.reader.load_images_from_dataurl_dict`
72
- and `nabu.io.utils.create_dict_of_indices`
73
-
74
-
75
- Notes
76
- ------
77
- Usually, when doing a scan, only one or a few darks/flats are acquired.
78
- However, the flat-field normalization has to be performed on each radio,
79
- although incoming beam can fluctuate between projections.
80
- The usual way to overcome this is to interpolate between flats.
81
- If interpolation="nearest", the first flat is used for the first
82
- radios subset, the second flat is used for the second radios subset,
83
- and so on.
84
- If interpolation="linear", the normalization is done as a linear
85
- function of the radio index.
86
-
87
- The normalization with synchrotron electric current is done as follows.
88
- Let s = sr/sr_max denote the ratio between current and maximum current,
89
- D be the dark-current frame, and X' be the normalized frame. Then:
90
- srcurrent_normalization(X) = X' = (X - D)/s + D
91
- flatfield_normalization(X') = (X' - D)/(F' - D) = (X - D) / (F - D) * sF/sX
92
- So current normalization boils down to a scalar multiplication after flat-field.
93
- """
94
- if self._full_shape:
95
- # this is never going to happen in this base class. But in the derived class for helical
96
- # which needs to keep the full shape
97
- if radios_indices is not None:
98
- radios_shape = (len(radios_indices),) + radios_shape[1:]
99
-
100
- self._set_parameters(radios_shape, radios_indices, interpolation, nan_value)
101
- self._set_flats_and_darks(flats, darks)
102
- self._precompute_flats_indices_weights()
103
- self._configure_srcurrent_normalization(radios_srcurrent, flats_srcurrent)
104
- self.distortion_correction = distortion_correction
105
- self.n_threads = min(1, get_num_threads(n_threads) // 2)
106
-
107
- def _set_parameters(self, radios_shape, radios_indices, interpolation, nan_value):
108
- self._set_radios_shape(radios_shape)
109
- if radios_indices is None:
110
- radios_indices = np.arange(0, self.n_radios, dtype=np.int32)
111
- else:
112
- radios_indices = np.array(radios_indices, dtype=np.int32)
113
- self._check_radios_and_indices_congruence(radios_indices)
114
-
115
- self.radios_indices = radios_indices
116
- self.interpolation = interpolation
117
- check_supported(interpolation, self._supported_interpolations, "Interpolation mode")
118
- self.nan_value = nan_value
119
- self._radios_idx_to_pos = dict(zip(self.radios_indices, np.arange(self.radios_indices.size)))
120
-
121
- def _set_radios_shape(self, radios_shape):
122
- if len(radios_shape) == 2:
123
- self.radios_shape = (1,) + radios_shape
124
- elif len(radios_shape) == 3:
125
- self.radios_shape = radios_shape
126
- else:
127
- raise ValueError("Expected radios to have 2 or 3 dimensions")
128
- n_radios, n_z, n_x = self.radios_shape
129
- self.n_radios = n_radios
130
- self.n_angles = n_radios
131
- self.shape = (n_z, n_x)
132
-
133
- def _set_flats_and_darks(self, flats, darks):
134
- self._check_frames(flats, "flats", 1, 9999)
135
- self.n_flats = len(flats)
136
- self.flats = flats
137
- self._sorted_flat_indices = sorted(self.flats.keys())
138
-
139
- if self._full_shape:
140
- # this is never going to happen in this base class. But in the derived class for helical
141
- # which needs to keep the full shape
142
- self.shape = flats[self._sorted_flat_indices[0]].shape
143
-
144
- self._flat2arrayidx = dict(zip(self._sorted_flat_indices, np.arange(self.n_flats)))
145
- self.flats_arr = np.zeros((self.n_flats,) + self.shape, "f")
146
- for i, idx in enumerate(self._sorted_flat_indices):
147
- self.flats_arr[i] = self.flats[idx]
148
-
149
- self._check_frames(darks, "darks", 1, 1)
150
- self.darks = darks
151
- self.n_darks = len(darks)
152
- self._sorted_dark_indices = sorted(self.darks.keys())
153
- self._dark = None
154
-
155
- def _check_frames(self, frames, frames_type, min_frames_required, max_frames_supported):
156
- n_frames = len(frames)
157
- if n_frames < min_frames_required:
158
- raise ValueError("Need at least %d %s" % (min_frames_required, frames_type))
159
- if n_frames > max_frames_supported:
160
- raise ValueError(
161
- "Flat-fielding with more than %d %s is not supported" % (max_frames_supported, frames_type)
162
- )
163
- self._check_frame_shape(frames, frames_type)
164
-
165
- def _check_frame_shape(self, frames, frames_type):
166
- for frame_idx, frame in frames.items():
167
- if frame.shape != self.shape:
168
- raise ValueError(
169
- "Invalid shape for %s %s: expected %s, but got %s"
170
- % (frames_type, frame_idx, str(self.shape), str(frame.shape))
171
- )
172
-
173
- def _check_radios_and_indices_congruence(self, radios_indices):
174
- if radios_indices.size != self.n_radios:
175
- raise ValueError(
176
- "Expected radios_indices to have length %s = n_radios, but got length %d"
177
- % (self.n_radios, radios_indices.size)
178
- )
179
-
180
- def _precompute_flats_indices_weights(self):
181
- """
182
- Build two arrays: "indices" and "weights".
183
- These arrays contain pre-computed information so that the interpolated flat is obtained with
184
-
185
- flat_interpolated = weight_prev * flat_prev + weight_next * flat_next
186
-
187
- where
188
- weight_prev, weight_next = weights[2*i], weights[2*i+1]
189
- idx_prev, idx_next = indices[2*i], indices[2*i+1]
190
- flat_prev, flat_next = flats[idx_prev], flats[idx_next]
191
-
192
- In words:
193
- - If a projection has an index between two flats, the equivalent flat is a linear interpolation
194
- between "previous flat" and "next flat".
195
- - If a projection has the same index as a flat, only this flat is used for normalization
196
- (this case normally never occurs, but it's handled in the code)
197
- """
198
-
199
- def _interp_linear(idx, prev_next):
200
- if len(prev_next) == 1: # current index corresponds to an acquired flat
201
- weights = (1, 0)
202
- f_idx = (self._flat2arrayidx[prev_next[0]], -1)
203
- else:
204
- prev_idx, next_idx = prev_next
205
- delta = next_idx - prev_idx
206
- w1 = 1 - (idx - prev_idx) / delta
207
- w2 = 1 - (next_idx - idx) / delta
208
- weights = (w1, w2)
209
- f_idx = (self._flat2arrayidx[prev_idx], self._flat2arrayidx[next_idx])
210
- return f_idx, weights
211
-
212
- def _interp_nearest(idx, prev_next):
213
- if len(prev_next) == 1: # current index corresponds to an acquired flat
214
- weights = (1, 0)
215
- f_idx = (self._flat2arrayidx[prev_next[0]], -1)
216
- else:
217
- prev_idx, next_idx = prev_next
218
- idx_to_take = prev_idx if abs(idx - prev_idx) < abs(idx - next_idx) else next_idx
219
- weights = (1, 0)
220
- f_idx = (self._flat2arrayidx[idx_to_take], -1)
221
- return f_idx, weights
222
-
223
- self.flats_idx = np.zeros((self.n_radios, 2), dtype=np.int32)
224
- self.flats_weights = np.zeros((self.n_radios, 2), dtype=np.float32)
225
- for i, idx in enumerate(self.radios_indices):
226
- prev_next = self.get_previous_next_indices(self._sorted_flat_indices, idx)
227
- if self.interpolation == "nearest":
228
- f_idx, weights = _interp_nearest(idx, prev_next)
229
- elif self.interpolation == "linear":
230
- f_idx, weights = _interp_linear(idx, prev_next)
231
- self.flats_idx[i] = f_idx
232
- self.flats_weights[i] = weights
233
-
234
- # pylint: disable=E1307
235
- def _configure_srcurrent_normalization(self, radios_srcurrent, flats_srcurrent):
236
- self.normalize_srcurrent = False
237
- if radios_srcurrent is None or flats_srcurrent is None:
238
- return
239
- radios_srcurrent = np.array(radios_srcurrent)
240
- if radios_srcurrent.size != self.n_radios:
241
- raise ValueError(
242
- "Expected 'radios_srcurrent' to have %d elements but got %d" % (self.n_radios, radios_srcurrent.size)
243
- )
244
- flats_srcurrent = np.array(flats_srcurrent)
245
- if flats_srcurrent.size != self.n_flats:
246
- raise ValueError(
247
- "Expected 'flats_srcurrent' to have %d elements but got %d" % (self.n_flats, flats_srcurrent.size)
248
- )
249
- self.normalize_srcurrent = True
250
- self.radios_srcurrent = radios_srcurrent
251
- self.flats_srcurrent = flats_srcurrent
252
- self.srcurrent_ratios = np.zeros(self.n_radios, "f")
253
- # Flats SRCurrent is obtained with "nearest" interp, to emulate an already-done flats SR current normalization
254
- for i, radio_idx in enumerate(self.radios_indices):
255
- flat_idx = self.get_nearest_index(self._sorted_flat_indices, radio_idx)
256
- flat_srcurrent = self.flats_srcurrent[self._flat2arrayidx[flat_idx]]
257
- self.srcurrent_ratios[i] = flat_srcurrent / self.radios_srcurrent[i]
258
-
259
- @staticmethod
260
- def get_previous_next_indices(arr, idx):
261
- pos = bisect_left(arr, idx)
262
- if pos == len(arr): # outside range
263
- return (arr[-1],)
264
- if arr[pos] == idx:
265
- return (idx,)
266
- if pos == 0:
267
- return (arr[0],)
268
- return arr[pos - 1], arr[pos]
269
-
270
- @staticmethod
271
- def get_nearest_index(arr, idx):
272
- pos = bisect_left(arr, idx)
273
- if pos == len(arr) or arr[pos] == idx:
274
- return arr[-1]
275
- return arr[pos - 1] if idx - arr[pos - 1] < arr[pos] - idx else arr[pos]
276
-
277
- @staticmethod
278
- def interp(pos, indices, weights, array, slice_y=slice(None, None), slice_x=slice(None, None)):
279
- """
280
- Interpolate between two values. The interpolator consists in pre-computed arrays such that
281
-
282
- prev, next = indices[pos]
283
- w1, w2 = weights[pos]
284
- interpolated_value = w1 * array[prev] + w2 * array[next]
285
- """
286
- prev_idx = indices[pos, 0]
287
- next_idx = indices[pos, 1]
288
-
289
- if slice_y != slice(None, None) or slice_x != slice(None, None):
290
- w1 = weights[pos, 0][slice_y, slice_x]
291
- w2 = weights[pos, 1][slice_y, slice_x]
292
- else:
293
- w1 = weights[pos, 0]
294
- w2 = weights[pos, 1]
295
-
296
- if next_idx == -1:
297
- val = array[prev_idx]
298
- else:
299
- val = w1 * array[prev_idx] + w2 * array[next_idx]
300
- return val
301
-
302
- def get_flat(self, pos, dtype=np.float32, slice_y=slice(None, None), slice_x=slice(None, None)):
303
- flat = self.interp(pos, self.flats_idx, self.flats_weights, self.flats_arr, slice_y=slice_y, slice_x=slice_x)
304
- if flat.dtype != dtype:
305
- flat = np.ascontiguousarray(flat, dtype=dtype)
306
- return flat
307
-
308
- def get_dark(self):
309
- if self._dark is None:
310
- first_dark_idx = self._sorted_dark_indices[0]
311
- dark = np.ascontiguousarray(self.darks[first_dark_idx], dtype=np.float32)
312
- self._dark = dark
313
- return self._dark
314
-
315
- def remove_invalid_values(self, img):
316
- if self.nan_value is None:
317
- return
318
- invalid_mask = np.logical_not(np.isfinite(img))
319
- img[invalid_mask] = self.nan_value
320
-
321
- def normalize_radios(self, radios):
322
- """
323
- Apply a flat-field normalization, with the current parameters, to a stack
324
- of radios.
325
- The processing is done in-place, meaning that the radios content is overwritten.
326
-
327
- Parameters
328
- -----------
329
- radios: numpy.ndarray
330
- Radios chunk
331
- """
332
- do_flats_distortion_correction = self.distortion_correction is not None
333
- dark = self.get_dark()
334
-
335
- def apply_flatfield(i):
336
- radio_data = radios[i]
337
- radio_data -= dark
338
- flat = self.get_flat(i)
339
- flat = flat - dark
340
- if do_flats_distortion_correction:
341
- flat = self.distortion_correction.estimate_and_correct(flat, radio_data)
342
- np.divide(radio_data, flat, out=radio_data)
343
- self.remove_invalid_values(radio_data)
344
-
345
- if self.n_threads > 2:
346
- with ThreadPool(self.n_threads) as tp:
347
- tp.map(apply_flatfield, range(self.n_radios))
348
- else:
349
- for i in range(self.n_radios):
350
- apply_flatfield(i)
351
-
352
- if self.normalize_srcurrent:
353
- radios *= self.srcurrent_ratios[:, np.newaxis, np.newaxis]
354
- return radios
355
-
356
- def normalize_single_radio(
357
- self, radio, radio_idx, dtype=np.float32, slice_y=slice(None, None), slice_x=slice(None, None)
358
- ):
359
- """
360
- Apply a flat-field normalization to a single projection image.
361
- """
362
- dark = self.get_dark()[slice_y, slice_x]
363
- radio -= dark
364
- radio_pos = self._radios_idx_to_pos[radio_idx]
365
- flat = self.get_flat(radio_pos, dtype=dtype, slice_y=slice_y, slice_x=slice_x)
366
- flat = flat - dark
367
- if self.distortion_correction is not None:
368
- flat = self.distortion_correction.estimate_and_correct(flat, radio)
369
- radio /= flat
370
- if self.normalize_srcurrent:
371
- radio *= self.srcurrent_ratios[radio_pos]
372
- self.remove_invalid_values(radio)
373
- return radio
374
-
375
-
376
- FlatField = FlatFieldArrays
377
-
378
-
379
- class FlatFieldDataUrls(FlatField):
380
- def __init__(
381
- self,
382
- radios_shape: tuple,
383
- flats: dict,
384
- darks: dict,
385
- radios_indices=None,
386
- interpolation: str = "linear",
387
- distortion_correction=None,
388
- nan_value=1.0,
389
- radios_srcurrent=None,
390
- flats_srcurrent=None,
391
- **chunk_reader_kwargs,
392
- ):
393
- """
394
- Initialize a flat-field normalization process with DataUrls.
395
-
396
- Parameters
397
- ----------
398
- radios_shape: tuple
399
- A tuple describing the shape of the radios stack, in the form
400
- `(n_radios, n_z, n_x)`.
401
- flats: dict
402
- Dictionary where the key is the flat index, and the value is a
403
- silx.io.DataUrl pointing to the flat.
404
- darks: dict
405
- Dictionary where the key is the dark index, and the value is a
406
- silx.io.DataUrl pointing to the dark.
407
- radios_indices: array, optional
408
- Array containing the radios indices. `radios_indices[0]` is the index
409
- of the first radio, and so on.
410
- interpolation: str, optional
411
- Interpolation method for flat-field. See below for more details.
412
- distortion_correction: DistortionCorrection, optional
413
- A DistortionCorrection object. If provided, it is used to correct flat distortions based on each radio.
414
- nan_value: float, optional
415
- Which float value is used to replace nan/inf after flat-field.
416
-
417
-
418
- Other Parameters
419
- ----------------
420
- The other named parameters are passed to ChunkReader(). Please read its
421
- documentation for more information.
422
-
423
- Notes
424
- ------
425
- Usually, when doing a scan, only one or a few darks/flats are acquired.
426
- However, the flat-field normalization has to be performed on each radio,
427
- although incoming beam can fluctuate between projections.
428
- The usual way to overcome this is to interpolate between flats.
429
- If interpolation="nearest", the first flat is used for the first
430
- radios subset, the second flat is used for the second radios subset,
431
- and so on.
432
- If interpolation="linear", the normalization is done as a linear
433
- function of the radio index.
434
- """
435
-
436
- flats_arrays_dict = load_images_from_dataurl_dict(flats, **chunk_reader_kwargs)
437
- darks_arrays_dict = load_images_from_dataurl_dict(darks, **chunk_reader_kwargs)
438
- super().__init__(
439
- radios_shape,
440
- flats_arrays_dict,
441
- darks_arrays_dict,
442
- radios_indices=radios_indices,
443
- interpolation=interpolation,
444
- distortion_correction=distortion_correction,
445
- nan_value=nan_value,
446
- radios_srcurrent=radios_srcurrent,
447
- flats_srcurrent=flats_srcurrent,
448
- )
@@ -1,144 +0,0 @@
1
- import numpy as np
2
-
3
- from nabu.cuda.processing import CudaProcessing
4
- from ..preproc.flatfield import FlatFieldArrays
5
- from ..utils import get_cuda_srcfile
6
- from ..io.reader import load_images_from_dataurl_dict
7
- from ..cuda.utils import __has_pycuda__
8
-
9
-
10
- class CudaFlatFieldArrays(FlatFieldArrays):
11
- def __init__(
12
- self,
13
- radios_shape,
14
- flats,
15
- darks,
16
- radios_indices=None,
17
- interpolation="linear",
18
- distortion_correction=None,
19
- nan_value=1.0,
20
- radios_srcurrent=None,
21
- flats_srcurrent=None,
22
- cuda_options=None,
23
- ):
24
- """
25
- Initialize a flat-field normalization CUDA process.
26
- Please read the documentation of nabu.preproc.flatfield.FlatField for help
27
- on the parameters.
28
- """
29
- #
30
- if distortion_correction is not None:
31
- raise NotImplementedError("Flats distortion correction is not implemented with the Cuda backend")
32
- #
33
- super().__init__(
34
- radios_shape,
35
- flats,
36
- darks,
37
- radios_indices=radios_indices,
38
- interpolation=interpolation,
39
- distortion_correction=distortion_correction,
40
- radios_srcurrent=radios_srcurrent,
41
- flats_srcurrent=flats_srcurrent,
42
- nan_value=nan_value,
43
- )
44
- self.cuda_processing = CudaProcessing(**(cuda_options or {}))
45
- self._init_cuda_kernels()
46
- self._load_flats_and_darks_on_gpu()
47
-
48
- def _init_cuda_kernels(self):
49
- # TODO
50
- if self.interpolation != "linear":
51
- raise ValueError("Interpolation other than linar is not yet implemented in the cuda back-end")
52
- #
53
- self._cuda_fname = get_cuda_srcfile("flatfield.cu")
54
- options = [
55
- "-DN_FLATS=%d" % self.n_flats,
56
- "-DN_DARKS=%d" % self.n_darks,
57
- ]
58
- if self.nan_value is not None:
59
- options.append("-DNAN_VALUE=%f" % self.nan_value)
60
- self.cuda_kernel = self.cuda_processing.kernel(
61
- "flatfield_normalization", self._cuda_fname, signature="PPPiiiPP", options=options
62
- )
63
- self._nx = np.int32(self.shape[1])
64
- self._ny = np.int32(self.shape[0])
65
-
66
- def _load_flats_and_darks_on_gpu(self):
67
- # Flats
68
- self.d_flats = self.cuda_processing.allocate_array("d_flats", (self.n_flats,) + self.shape, np.float32)
69
- for i, flat_idx in enumerate(self._sorted_flat_indices):
70
- self.d_flats[i].set(np.ascontiguousarray(self.flats[flat_idx], dtype=np.float32))
71
- # Darks
72
- self.d_darks = self.cuda_processing.allocate_array("d_darks", (self.n_darks,) + self.shape, np.float32)
73
- for i, dark_idx in enumerate(self._sorted_dark_indices):
74
- self.d_darks[i].set(np.ascontiguousarray(self.darks[dark_idx], dtype=np.float32))
75
- self.d_darks_indices = self.cuda_processing.to_device(
76
- "d_darks_indices", np.array(self._sorted_dark_indices, dtype=np.int32)
77
- )
78
- # Indices
79
- self.d_flats_indices = self.cuda_processing.to_device("d_flats_indices", self.flats_idx)
80
- self.d_flats_weights = self.cuda_processing.to_device("d_flats_weights", self.flats_weights)
81
-
82
- def normalize_radios(self, radios):
83
- """
84
- Apply a flat-field correction, with the current parameters, to a stack
85
- of radios.
86
-
87
- Parameters
88
- -----------
89
- radios_shape: `pycuda.gpuarray.GPUArray`
90
- Radios chunk.
91
- """
92
- if not (isinstance(radios, self.cuda_processing.array_class)):
93
- raise ValueError("Expected a pycuda.gpuarray (got %s)" % str(type(radios)))
94
- if radios.dtype != np.float32:
95
- raise ValueError("radios must be in float32 dtype (got %s)" % str(radios.dtype))
96
- if radios.shape != self.radios_shape:
97
- raise ValueError("Expected radios shape = %s but got %s" % (str(self.radios_shape), str(radios.shape)))
98
- self.cuda_kernel(
99
- radios,
100
- self.d_flats,
101
- self.d_darks,
102
- self._nx,
103
- self._ny,
104
- np.int32(self.n_radios),
105
- self.d_flats_indices,
106
- self.d_flats_weights,
107
- )
108
- if self.normalize_srcurrent:
109
- for i in range(self.n_radios):
110
- radios[i] *= self.srcurrent_ratios[i]
111
- return radios
112
-
113
-
114
- CudaFlatField = CudaFlatFieldArrays
115
-
116
-
117
- class CudaFlatFieldDataUrls(CudaFlatField):
118
- def __init__(
119
- self,
120
- radios_shape,
121
- flats,
122
- darks,
123
- radios_indices=None,
124
- interpolation="linear",
125
- distortion_correction=None,
126
- nan_value=1.0,
127
- radios_srcurrent=None,
128
- flats_srcurrent=None,
129
- cuda_options=None,
130
- **chunk_reader_kwargs,
131
- ):
132
- flats_arrays_dict = load_images_from_dataurl_dict(flats, **chunk_reader_kwargs)
133
- darks_arrays_dict = load_images_from_dataurl_dict(darks, **chunk_reader_kwargs)
134
- super().__init__(
135
- radios_shape,
136
- flats_arrays_dict,
137
- darks_arrays_dict,
138
- radios_indices=radios_indices,
139
- interpolation=interpolation,
140
- distortion_correction=distortion_correction,
141
- radios_srcurrent=radios_srcurrent,
142
- flats_srcurrent=flats_srcurrent,
143
- cuda_options=cuda_options,
144
- )
@@ -1,79 +0,0 @@
1
- import numpy as np
2
- from .flatfield import FlatFieldArrays, load_images_from_dataurl_dict, check_supported
3
-
4
-
5
- class FlatFieldArraysVariableRegion(FlatFieldArrays):
6
- _full_shape = True
7
-
8
- def _check_frame_shape(self, frames, frames_type):
9
- # in helical the flat is the whole one and its shape does not necesseraly match the smaller frames.
10
- # Therefore no check is done to allow this.
11
- pass
12
-
13
- def _check_radios_and_indices_congruence(self, radios_indices):
14
- """At variance with parent class, preprocesing is done with on a fraction of the radios,
15
- whose length may vary. So we dont enforce here that the lenght is always the same
16
- """
17
- pass
18
-
19
- def _normalize_radios(self, radios, sub_indexes, sub_regions_per_radio):
20
- """
21
- Apply a flat-field normalization, with the current parameters, to a stack
22
- of radios.
23
- The processing is done in-place, meaning that the radios content is overwritten.
24
- """
25
- if len(sub_regions_per_radio) != len(sub_indexes):
26
- message = f""" The length of sub_regions_per_radio,which is {len(sub_regions_per_radio)} ,
27
- does not correspond to the length of sub_indexes which is {len(sub_indexes)}
28
- """
29
- raise ValueError(message)
30
- do_flats_distortion_correction = self.distortion_correction is not None
31
-
32
- whole_dark = self.get_dark()
33
- for i, (idx, sub_r) in enumerate(zip(sub_indexes, sub_regions_per_radio)):
34
- start_x, end_x, start_y, end_y = sub_r
35
- slice_x = slice(start_x, end_x)
36
- slice_y = slice(start_y, end_y)
37
-
38
- self.normalize_single_radio(radios[i], idx, dtype=np.float32, slice_y=slice_y, slice_x=slice_x)
39
-
40
- return radios
41
-
42
-
43
- class FlatFieldDataVariableRegionUrls(FlatFieldArraysVariableRegion):
44
- def __init__(
45
- self,
46
- radios_shape: tuple,
47
- flats: dict,
48
- darks: dict,
49
- radios_indices=None,
50
- interpolation: str = "linear",
51
- distortion_correction=None,
52
- nan_value=1.0,
53
- radios_srcurrent=None,
54
- flats_srcurrent=None,
55
- **chunk_reader_kwargs,
56
- ):
57
- flats_arrays_dict = load_images_from_dataurl_dict(flats, **chunk_reader_kwargs)
58
- darks_arrays_dict = load_images_from_dataurl_dict(darks, **chunk_reader_kwargs)
59
-
60
- _flats_indexes = list(flats_arrays_dict.keys())
61
- _flats_indexes.sort()
62
-
63
- self.flats_indexes = np.array(_flats_indexes)
64
- self.flats_stack = np.array([flats_arrays_dict[i] for i in self.flats_indexes], "f")
65
-
66
- flats_arrays_dict = dict([[indx, flat] for indx, flat in zip(self.flats_indexes, self.flats_stack)])
67
-
68
- super().__init__(
69
- radios_shape,
70
- flats_arrays_dict,
71
- darks_arrays_dict,
72
- radios_indices=radios_indices,
73
- interpolation=interpolation,
74
- distortion_correction=distortion_correction,
75
- nan_value=nan_value,
76
- radios_srcurrent=radios_srcurrent,
77
- flats_srcurrent=flats_srcurrent,
78
- )
79
- self._sorted_flat_indices = np.array(self._sorted_flat_indices, "i")