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
@@ -1,220 +0,0 @@
1
- import numpy as np
2
- import pytest
3
- from nabu.reconstruction.rings_cuda import CudaSinoMeanDeringer
4
- from nabu.testutils import compare_arrays, get_data, generate_tests_scenarios, __do_long_tests__
5
- from nabu.reconstruction.rings import MunchDeringer, SinoMeanDeringer, VoDeringer, __has_algotom__
6
- from nabu.thirdparty.pore3d_deringer_munch import munchetal_filter
7
- from nabu.cuda.utils import __has_pycuda__, get_cuda_context
8
-
9
- if __has_pycuda__:
10
- import pycuda.gpuarray as garray
11
- from nabu.processing.fft_cuda import get_available_fft_implems
12
- from nabu.reconstruction.rings_cuda import (
13
- CudaMunchDeringer,
14
- can_use_cuda_deringer,
15
- CudaVoDeringer,
16
- __have_tomocupy_deringer__,
17
- )
18
-
19
- __has_cuda_deringer__ = can_use_cuda_deringer()
20
- else:
21
- __has_cuda_deringer__ = False
22
- __have_tomocupy_deringer__ = False
23
-
24
- fw_scenarios = generate_tests_scenarios(
25
- {
26
- "levels": [4],
27
- "sigma": [1.0],
28
- "wname": ["db15"],
29
- "padding": [(100, 100)],
30
- "fft_implem": ["skcuda"],
31
- }
32
- )
33
- if __do_long_tests__:
34
- fw_scenarios = generate_tests_scenarios(
35
- {
36
- "levels": [4, 2],
37
- "sigma": [1.0, 2.0],
38
- "wname": ["db15", "haar", "rbio4.4"],
39
- "padding": [None, (100, 100), (50, 71)],
40
- "fft_implem": ["skcuda", "vkfft"],
41
- }
42
- )
43
-
44
-
45
- @pytest.fixture(scope="class")
46
- def bootstrap(request):
47
- cls = request.cls
48
- cls.sino = get_data("mri_sino500.npz")["data"]
49
- cls.sino2 = get_data("sino_bamboo_hercules.npz")["data"]
50
- cls.tol = 5e-3
51
- cls.rings = {150: 0.5, -150: 0.5}
52
- if __has_pycuda__:
53
- cls.ctx = get_cuda_context(cleanup_at_exit=False)
54
- cls._available_fft_implems = get_available_fft_implems()
55
- yield
56
- if __has_pycuda__:
57
- cls.ctx.pop()
58
-
59
-
60
- @pytest.mark.usefixtures("bootstrap")
61
- class TestMunchDeringer:
62
- @staticmethod
63
- def add_stripes_to_sino(sino, rings_desc):
64
- """
65
- Create a new sinogram by adding synthetic stripes to an existing one.
66
-
67
- Parameters
68
- ----------
69
- sino: array-like
70
- Sinogram.
71
- rings_desc: dict
72
- Dictionary describing the stripes locations and intensity.
73
- The location is an integer in [0, N[ where N is the number of columns.
74
- The intensity is a float: percentage of the current column mean value.
75
- """
76
- sino_out = np.copy(sino)
77
- for loc, intensity in rings_desc.items():
78
- sino_out[:, loc] += sino[:, loc].mean() * intensity
79
- return sino_out
80
-
81
- @staticmethod
82
- def get_fourier_wavelets_reference_result(sino, config):
83
- # Reference destriping with pore3d "munchetal_filter"
84
- padding = config.get("padding", None)
85
- if padding is not None:
86
- sino = np.pad(sino, ((0, 0), padding), mode="edge")
87
- ref = munchetal_filter(sino, config["levels"], config["sigma"], wname=config["wname"])
88
- if config["padding"] is not None:
89
- ref = ref[:, padding[0] : -padding[1]]
90
- return ref
91
-
92
- @pytest.mark.skipif(munchetal_filter is None, reason="Need PyWavelets for this test")
93
- @pytest.mark.parametrize("config", fw_scenarios)
94
- def test_munch_deringer(self, config):
95
- deringer = MunchDeringer(
96
- config["sigma"], self.sino.shape, levels=config["levels"], wname=config["wname"], padding=config["padding"]
97
- )
98
- sino = self.add_stripes_to_sino(self.sino, self.rings)
99
- ref = self.get_fourier_wavelets_reference_result(sino, config)
100
- # Wrapping with DeRinger
101
- res = np.zeros((1,) + sino.shape, dtype=np.float32)
102
- deringer.remove_rings(sino, output=res)
103
-
104
- err_max = np.max(np.abs(res[0] - ref))
105
- assert err_max < self.tol, "Max error is too high"
106
-
107
- @pytest.mark.skipif(
108
- not (__has_cuda_deringer__) or munchetal_filter is None,
109
- reason="Need pycuda, pycudwt and (scikit-cuda or pyvkfft) for this test",
110
- )
111
- @pytest.mark.parametrize("config", fw_scenarios)
112
- def test_cuda_munch_deringer(self, config):
113
- fft_implem = config["fft_implem"]
114
- if fft_implem not in self._available_fft_implems:
115
- pytest.skip("FFT implementation %s is not available" % fft_implem)
116
- sino = self.add_stripes_to_sino(self.sino, self.rings)
117
- deringer = CudaMunchDeringer(
118
- config["sigma"],
119
- self.sino.shape,
120
- levels=config["levels"],
121
- wname=config["wname"],
122
- padding=config["padding"],
123
- fft_backend=fft_implem,
124
- cuda_options={"ctx": self.ctx},
125
- )
126
- d_sino = garray.to_gpu(sino)
127
- deringer.remove_rings(d_sino)
128
- res = d_sino.get()
129
-
130
- ref = self.get_fourier_wavelets_reference_result(sino, config)
131
-
132
- err_max = np.max(np.abs(res - ref))
133
- assert err_max < 1e-1, "Max error is too high with configuration %s" % (str(config))
134
-
135
- @pytest.mark.skipif(
136
- not (__has_algotom__),
137
- reason="Need algotom for this test",
138
- )
139
- def test_vo_deringer(self):
140
- deringer = VoDeringer(self.sino.shape)
141
- sino_deringed = deringer.remove_rings_sinogram(self.sino)
142
- sinos = np.tile(self.sino, (10, 1, 1))
143
- sinos_deringed = deringer.remove_rings_sinograms(sinos)
144
- # TODO check result. The generated test sinogram is "too synthetic" for this kind of deringer
145
-
146
- @pytest.mark.skipif(
147
- not (__have_tomocupy_deringer__),
148
- reason="Need cupy for this test",
149
- )
150
- def test_cuda_vo_deringer(self):
151
- # Beware, this deringer seems to be buggy for "too-small" sinograms
152
- # (NaNs on the edges and in some regions). To be investigated
153
-
154
- deringer = CudaVoDeringer(self.sino2.shape)
155
- d_sino = garray.to_gpu(self.sino2)
156
- deringer.remove_rings_sinogram(d_sino)
157
- sino = d_sino.get()
158
-
159
- if __has_algotom__:
160
- vo_deringer = VoDeringer(self.sino2.shape)
161
- sino_deringed = vo_deringer.remove_rings_sinogram(self.sino2)
162
-
163
- assert (
164
- np.max(np.abs(sino - sino_deringed)) < 2e-3
165
- ), "Cuda implementation of Vo deringer does not yield the same results as base implementation"
166
-
167
- def test_mean_deringer(self):
168
- deringer_no_filtering = SinoMeanDeringer(self.sino.shape, mode="subtract")
169
-
170
- sino = self.sino.copy()
171
- deringer_no_filtering.remove_rings_sinogram(sino)
172
-
173
- sino = self.sino.copy()
174
- deringer_with_filtering = SinoMeanDeringer(self.sino.shape, mode="subtract", filter_cutoff=(0, 30))
175
- deringer_with_filtering.remove_rings_sinogram(sino)
176
- # TODO check results
177
-
178
- @pytest.mark.skipif(not (__has_pycuda__), reason="Need pycuda for this test")
179
- def test_cuda_mean_deringer(self):
180
- cuda_deringer = CudaSinoMeanDeringer(
181
- self.sino.shape,
182
- mode="subtract",
183
- filter_cutoff=(
184
- 0,
185
- 10,
186
- ),
187
- ctx=self.ctx,
188
- )
189
- deringer = SinoMeanDeringer(
190
- self.sino.shape,
191
- mode="subtract",
192
- filter_cutoff=(
193
- 0,
194
- 10,
195
- ),
196
- )
197
-
198
- d_sino = cuda_deringer.processing.to_device("sino", self.sino)
199
- cuda_deringer.remove_rings_sinogram(d_sino)
200
-
201
- sino = self.sino.copy()
202
- sino_d = deringer.remove_rings_sinogram(sino)
203
-
204
- dirac = np.zeros(self.sino.shape[-1], "f")
205
- dirac[dirac.size // 2] = 1
206
- deringer_filter_response = deringer._apply_filter(dirac)
207
-
208
- d_dirac = cuda_deringer.processing.to_device("dirac", dirac)
209
- cuda_deringer_filter_response = cuda_deringer._apply_filter(d_dirac)
210
-
211
- is_close, residual = compare_arrays(
212
- deringer_filter_response, cuda_deringer_filter_response.get(), 1e-7, return_residual=True
213
- )
214
- assert is_close, "Cuda deringer does not have the correct filter response: max_error=%.2e" % residual
215
-
216
- # There is a rather large discrepancy between the vertical_mean kernel and numpy.mean(). Not sure who is right
217
- is_close, residual = compare_arrays(sino_d, d_sino.get(), 1e-1, return_residual=True)
218
- assert is_close, (
219
- "Cuda deringer does not yield the same result as base implementation: max_error=%.2e" % residual
220
- )
@@ -1,252 +0,0 @@
1
- import numpy as np
2
- import pytest
3
- from scipy.ndimage import shift
4
- from nabu.pipeline.params import fbp_filters
5
- from nabu.utils import clip_circle
6
- from nabu.testutils import get_data, generate_tests_scenarios, __do_long_tests__
7
- from nabu.cuda.utils import get_cuda_context, __has_pycuda__
8
- from nabu.opencl.utils import get_opencl_context, __has_pyopencl__
9
-
10
- from nabu.processing.fft_cuda import has_skcuda, has_vkfft as has_vkfft_cu
11
- from nabu.processing.fft_opencl import has_vkfft as has_vkfft_cl
12
-
13
- __has_pycuda__ = __has_pycuda__ and (has_skcuda() or has_vkfft_cu())
14
- __has_pyopencl__ = __has_pyopencl__ and has_vkfft_cl()
15
-
16
- if __has_pycuda__:
17
- from nabu.reconstruction.fbp import CudaBackprojector
18
- if __has_pyopencl__:
19
- from nabu.reconstruction.fbp_opencl import OpenCLBackprojector
20
-
21
-
22
- scenarios = generate_tests_scenarios({"backend": ["cuda", "opencl"]})
23
- if __do_long_tests__:
24
- scenarios = generate_tests_scenarios(
25
- {
26
- "backend": ["cuda", "opencl"],
27
- "input_on_gpu": [False, True],
28
- "output_on_gpu": [False, True],
29
- "use_textures": [True, False],
30
- }
31
- )
32
-
33
-
34
- @pytest.fixture(scope="class")
35
- def bootstrap(request):
36
- cls = request.cls
37
- cls.sino_512 = get_data("mri_sino500.npz")["data"]
38
- cls.ref_512 = get_data("mri_rec_astra.npz")["data"]
39
- # always use contiguous arrays
40
- cls.sino_511 = np.ascontiguousarray(cls.sino_512[:, :-1])
41
- # Could be set to 5.0e-2 when using textures. When not using textures, interpolation slightly differs
42
- cls.tol = 5.1e-2
43
-
44
- if __has_pycuda__:
45
- cls.cuda_ctx = get_cuda_context(cleanup_at_exit=False)
46
- if __has_pyopencl__:
47
- cls.opencl_ctx = get_opencl_context("all")
48
- yield
49
- if __has_pycuda__:
50
- cls.cuda_ctx.pop()
51
-
52
-
53
- @pytest.mark.usefixtures("bootstrap")
54
- class TestFBP:
55
- @staticmethod
56
- def clip_to_inner_circle(img, radius_factor=0.99):
57
- radius = int(radius_factor * max(img.shape) / 2)
58
- return clip_circle(img, radius=radius)
59
-
60
- def _get_backprojector(self, config, *bp_args, **bp_kwargs):
61
- if config["backend"] == "cuda":
62
- if not (__has_pycuda__):
63
- pytest.skip("Need pycuda + (scikit-cuda or pyvkfft)")
64
- Backprojector = CudaBackprojector
65
- ctx = self.cuda_ctx
66
- else:
67
- if not (__has_pyopencl__):
68
- pytest.skip("Need pyopencl + pyvkfft")
69
- Backprojector = OpenCLBackprojector
70
- ctx = self.opencl_ctx
71
- if config.get("use_textures", True) is False:
72
- # patch "extra_options"
73
- extra_options = bp_kwargs.pop("extra_options", {})
74
- extra_options["use_textures"] = False
75
- bp_kwargs["extra_options"] = extra_options
76
- return Backprojector(*bp_args, **bp_kwargs, backend_options={"ctx": ctx})
77
-
78
- @staticmethod
79
- def apply_fbp(config, backprojector, sinogram):
80
- if config.get("input_on_gpu", False):
81
- sinogram = backprojector._processing.set_array("sinogram", sinogram)
82
- if config.get("output_on_gpu", False):
83
- output = backprojector._processing.allocate_array("output", backprojector.slice_shape, dtype="f")
84
- else:
85
- output = None
86
- res = backprojector.fbp(sinogram, output=output)
87
- if config.get("output_on_gpu", False):
88
- res = res.get()
89
- return res
90
-
91
- @pytest.mark.parametrize("config", scenarios)
92
- def test_fbp_512(self, config):
93
- """
94
- Simple test of a FBP on a 512x512 slice
95
- """
96
- B = self._get_backprojector(config, (500, 512))
97
- res = self.apply_fbp(config, B, self.sino_512)
98
-
99
- delta_clipped = self.clip_to_inner_circle(res - self.ref_512)
100
- err_max = np.max(np.abs(delta_clipped))
101
-
102
- assert err_max < self.tol, "Something wrong with config=%s" % (str(config))
103
-
104
- @pytest.mark.parametrize("config", scenarios)
105
- def test_fbp_511(self, config):
106
- """
107
- Test FBP of a 511x511 slice where the rotation axis is at (512-1)/2.0
108
- """
109
- B = self._get_backprojector(config, (500, 511), rot_center=255.5)
110
- res = self.apply_fbp(config, B, self.sino_511)
111
- ref = self.ref_512[:-1, :-1]
112
-
113
- delta_clipped = self.clip_to_inner_circle(res - ref)
114
- err_max = np.max(np.abs(delta_clipped))
115
-
116
- assert err_max < self.tol, "Something wrong with config=%s" % (str(config))
117
-
118
- @pytest.mark.parametrize("config", scenarios)
119
- def test_fbp_roi(self, config):
120
- """
121
- Test FBP in region of interest
122
- """
123
- sino = self.sino_511
124
-
125
- B0 = self._get_backprojector(config, sino.shape, rot_center=255.5)
126
- ref = B0.fbp(sino)
127
-
128
- def backproject_roi(roi, reference):
129
- B = self._get_backprojector(config, sino.shape, rot_center=255.5, slice_roi=roi)
130
- res = self.apply_fbp(config, B, sino)
131
- err_max = np.max(np.abs(res - reference))
132
- return err_max
133
-
134
- cases = {
135
- # Test 1: use slice_roi=(0, -1, 0, -1), i.e plain FBP of whole slice
136
- 1: [(0, None, 0, None), ref],
137
- # Test 2: horizontal strip
138
- 2: [(0, None, 50, 55), ref[50:55, :]],
139
- # Test 3: vertical strip
140
- 3: [(60, 65, 0, None), ref[:, 60:65]],
141
- # Test 4: rectangular inner ROI
142
- 4: [(157, 162, 260, -10), ref[260:-10, 157:162]],
143
- }
144
- for roi, ref in cases.values():
145
- err_max = backproject_roi(roi, ref)
146
- assert err_max < self.tol, "Something wrong with ROI = %s for config=%s" % (
147
- str(roi),
148
- str(config),
149
- )
150
-
151
- @pytest.mark.parametrize("config", scenarios)
152
- def test_fbp_axis_corr(self, config):
153
- """
154
- Test the "axis correction" feature
155
- """
156
- sino = self.sino_512
157
-
158
- # Create a sinogram with a drift in the rotation axis
159
- def create_drifted_sino(sino, drifts):
160
- out = np.zeros_like(sino)
161
- for i in range(sino.shape[0]):
162
- out[i] = shift(sino[i], drifts[i])
163
- return out
164
-
165
- drifts = np.linspace(0, 20, sino.shape[0])
166
- sino = create_drifted_sino(sino, drifts)
167
-
168
- B = self._get_backprojector(config, sino.shape, extra_options={"axis_correction": drifts})
169
- res = self.apply_fbp(config, B, sino)
170
-
171
- delta_clipped = clip_circle(res - self.ref_512, radius=200)
172
- err_max = np.max(np.abs(delta_clipped))
173
- # Max error is relatively high, migh be due to interpolation of scipy shift in sinogram
174
- assert err_max < 10.0, "Max error is too high"
175
-
176
- @pytest.mark.parametrize("config", scenarios)
177
- def test_fbp_clip_circle(self, config):
178
- """
179
- Test the "clip outer circle" parameter in (extra options)
180
- """
181
- sino = self.sino_512
182
- tol = 1e-5
183
-
184
- for rot_center in [None, sino.shape[1] / 2.0 - 10, sino.shape[1] / 2.0 + 15]:
185
- B = self._get_backprojector(
186
- config, sino.shape, rot_center=rot_center, extra_options={"clip_outer_circle": True}
187
- )
188
- res = self.apply_fbp(config, B, sino)
189
-
190
- B0 = self._get_backprojector(
191
- config, sino.shape, rot_center=rot_center, extra_options={"clip_outer_circle": False}
192
- )
193
- res_noclip = B0.fbp(sino)
194
- ref = self.clip_to_inner_circle(res_noclip, radius_factor=1)
195
-
196
- abs_diff = np.abs(res - ref)
197
- err_max = np.max(abs_diff)
198
- assert err_max < tol, "Max error is too high for rot_center=%s ; %s" % (str(rot_center), str(config))
199
-
200
- @pytest.mark.parametrize("config", scenarios)
201
- def test_fbp_centered_axis(self, config):
202
- """
203
- Test the "centered_axis" parameter (in extra options)
204
- """
205
- sino = np.pad(self.sino_512, ((0, 0), (100, 0)))
206
- rot_center = (self.sino_512.shape[1] - 1) / 2.0 + 100
207
-
208
- B0 = self._get_backprojector(config, self.sino_512.shape)
209
- ref = B0.fbp(self.sino_512)
210
-
211
- # Check that "centered_axis" worked
212
-
213
- B = self._get_backprojector(config, sino.shape, rot_center=rot_center, extra_options={"centered_axis": True})
214
- res = self.apply_fbp(config, B, sino)
215
- # The outside region (outer circle) is different as "res" is a wider slice
216
- diff = self.clip_to_inner_circle(res[50:-50, 50:-50] - ref)
217
- err_max = np.max(np.abs(diff))
218
- assert err_max < 5e-2, "centered_axis without clip_circle: something wrong"
219
-
220
- # Check that "clip_outer_circle" works when used jointly with "centered_axis"
221
- B = self._get_backprojector(
222
- config,
223
- sino.shape,
224
- rot_center=rot_center,
225
- extra_options={
226
- "centered_axis": True,
227
- "clip_outer_circle": True,
228
- },
229
- )
230
- res2 = self.apply_fbp(config, B, sino)
231
- diff = res2 - self.clip_to_inner_circle(res, radius_factor=1)
232
- err_max = np.max(np.abs(diff))
233
- assert err_max < 1e-5, "centered_axis with clip_circle: something wrong"
234
-
235
- @pytest.mark.parametrize("config", scenarios)
236
- def test_fbp_filters(self, config):
237
- for filter_name in set(fbp_filters.values()):
238
- if filter_name in [None, "ramlak"]:
239
- continue
240
- B = self._get_backprojector(config, self.sino_512.shape, filter_name=filter_name)
241
- self.apply_fbp(config, B, self.sino_512)
242
- # not sure what to check in this case
243
-
244
- @pytest.mark.parametrize("config", scenarios)
245
- def test_differentiated_backprojection(self, config):
246
- # test Hilbert + DBP
247
- sino_diff = np.diff(self.sino_512, axis=1, prepend=0).astype("f")
248
- # Need to translate the axis a little bit, because of non-centered differentiation.
249
- # prepend -> +0.5 ; append -> -0.5
250
- B = self._get_backprojector(config, sino_diff.shape, filter_name="hilbert", rot_center=255.5 + 0.5)
251
- rec = self.apply_fbp(config, B, sino_diff)
252
- # Looks good, but all frequencies are not recovered. Use a metric like SSIM or FRC ?
@@ -1,133 +0,0 @@
1
- import numpy as np
2
- import pytest
3
- from nabu.reconstruction.filtering import SinoFilter, filter_sinogram
4
- from nabu.cuda.utils import __has_pycuda__
5
- from nabu.opencl.utils import __has_pyopencl__
6
- from nabu.testutils import get_data, generate_tests_scenarios, __do_long_tests__
7
-
8
- if __has_pycuda__:
9
- from nabu.cuda.utils import get_cuda_context
10
- from nabu.reconstruction.filtering_cuda import CudaSinoFilter
11
- import pycuda.gpuarray as garray
12
- if __has_pyopencl__:
13
- import pyopencl.array as parray
14
- from nabu.opencl.processing import OpenCLProcessing
15
- from nabu.reconstruction.filtering_opencl import OpenCLSinoFilter, __has_vkfft__
16
-
17
- filters_to_test = ["ramlak", "shepp-logan", "tukey"]
18
- padding_modes_to_test = ["constant", "edge"]
19
- if __do_long_tests__:
20
- filters_to_test = ["ramlak", "shepp-logan", "cosine", "hamming", "hann", "tukey", "lanczos"]
21
- padding_modes_to_test = SinoFilter.available_padding_modes
22
-
23
- tests_scenarios = generate_tests_scenarios(
24
- {
25
- "filter_name": filters_to_test,
26
- "padding_mode": padding_modes_to_test,
27
- "output_provided": [True, False],
28
- }
29
- )
30
-
31
-
32
- @pytest.fixture(scope="class")
33
- def bootstrap(request):
34
- cls = request.cls
35
- cls.sino = get_data("mri_sino500.npz")["data"]
36
- if __has_pycuda__:
37
- cls.ctx_cuda = get_cuda_context(cleanup_at_exit=False)
38
- cls.sino_cuda = garray.to_gpu(cls.sino)
39
- if __has_pyopencl__:
40
- cls.cl = OpenCLProcessing(device_type="all")
41
- cls.sino_cl = parray.to_device(cls.cl.queue, cls.sino)
42
-
43
- yield
44
-
45
- if __has_pycuda__:
46
- cls.ctx_cuda.pop()
47
-
48
-
49
- @pytest.mark.usefixtures("bootstrap")
50
- class TestSinoFilter:
51
- @pytest.mark.parametrize("config", tests_scenarios)
52
- def test_filter(self, config):
53
- sino = self.sino
54
-
55
- sino_filter = SinoFilter(
56
- sino.shape,
57
- filter_name=config["filter_name"],
58
- padding_mode=config["padding_mode"],
59
- )
60
- if config["output_provided"]:
61
- output = np.zeros_like(sino)
62
- else:
63
- output = None
64
- res = sino_filter.filter_sino(sino, output=output)
65
- if output is not None:
66
- assert id(res) == id(output), "when providing output, return value must not change"
67
-
68
- ref = filter_sinogram(
69
- sino, sino_filter.dwidth_padded, filter_name=config["filter_name"], padding_mode=config["padding_mode"]
70
- )
71
-
72
- assert np.allclose(res, ref, atol=1e-6)
73
-
74
- @pytest.mark.skipif(not (__has_pycuda__), reason="Need Cuda + pycuda to use CudaSinoFilter")
75
- @pytest.mark.parametrize("config", tests_scenarios)
76
- def test_cuda_filter(self, config):
77
- sino = self.sino_cuda
78
-
79
- sino_filter = CudaSinoFilter(
80
- sino.shape,
81
- filter_name=config["filter_name"],
82
- padding_mode=config["padding_mode"],
83
- cuda_options={"ctx": self.ctx_cuda},
84
- )
85
- if config["output_provided"]:
86
- output = garray.zeros(sino.shape, "f")
87
- else:
88
- output = None
89
- res = sino_filter.filter_sino(sino, output=output)
90
- if output is not None:
91
- assert id(res) == id(output), "when providing output, return value must not change"
92
-
93
- ref = filter_sinogram(
94
- self.sino, sino_filter.dwidth_padded, filter_name=config["filter_name"], padding_mode=config["padding_mode"]
95
- )
96
-
97
- if not np.allclose(res.get(), ref, atol=6e-5):
98
- from spire.utils import ims
99
-
100
- ims([res.get(), ref, res.get() - ref])
101
-
102
- assert np.allclose(res.get(), ref, atol=6e-5), "test_cuda_filter: something wrong with config=%s" % (
103
- str(config)
104
- )
105
-
106
- @pytest.mark.skipif(
107
- not (__has_pyopencl__ and __has_vkfft__), reason="Need OpenCL + pyopencl + pyvkfft to use OpenCLSinoFilter"
108
- )
109
- @pytest.mark.parametrize("config", tests_scenarios)
110
- def test_opencl_filter(self, config):
111
- sino = self.sino_cl
112
-
113
- sino_filter = OpenCLSinoFilter(
114
- sino.shape,
115
- filter_name=config["filter_name"],
116
- padding_mode=config["padding_mode"],
117
- opencl_options={"ctx": self.cl.ctx},
118
- )
119
- if config["output_provided"]:
120
- output = parray.zeros(self.cl.queue, sino.shape, "f")
121
- else:
122
- output = None
123
- res = sino_filter.filter_sino(sino, output=output)
124
- if output is not None:
125
- assert id(res) == id(output), "when providing output, return value must not change"
126
-
127
- ref = filter_sinogram(
128
- self.sino, sino_filter.dwidth_padded, filter_name=config["filter_name"], padding_mode=config["padding_mode"]
129
- )
130
-
131
- assert np.allclose(res.get(), ref, atol=6e-5), "test_opencl_filter: something wrong with config=%s" % (
132
- str(config)
133
- )