nabu 2024.1.1__py3-none-any.whl → 2024.1.2__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (2095) hide show
  1. nabu/__init__.py +1 -1
  2. nabu/app/cast_volume.py +11 -2
  3. nabu/app/multicor.py +24 -2
  4. nabu/io/cast_volume.py +3 -3
  5. nabu/io/utils.py +2 -2
  6. nabu/stitching/tests/test_z_stitching.py +0 -1
  7. nabu/stitching/z_stitching.py +3 -3
  8. {nabu-2024.1.1.dist-info → nabu-2024.1.2.dist-info}/METADATA +2 -2
  9. nabu-2024.1.2.dist-info/RECORD +296 -0
  10. {nabu-2024.1.1.dist-info → nabu-2024.1.2.dist-info}/WHEEL +1 -1
  11. nabu-2024.1.2.dist-info/top_level.txt +2 -0
  12. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/doc/conf.py +0 -137
  13. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/doc/create_conf_doc.py +0 -38
  14. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/doc/get_mathjax.py +0 -34
  15. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/__init__.py +0 -17
  16. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/bootstrap.py +0 -88
  17. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/bootstrap_stitching.py +0 -69
  18. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/cast_volume.py +0 -272
  19. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/cli_configs.py +0 -626
  20. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/compare_volumes.py +0 -94
  21. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/composite_cor.py +0 -144
  22. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/correct_rot.py +0 -70
  23. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/create_distortion_map_from_poly.py +0 -153
  24. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/diag_to_pix.py +0 -358
  25. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/diag_to_rot.py +0 -449
  26. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/double_flatfield.py +0 -143
  27. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/generate_header.py +0 -261
  28. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/histogram.py +0 -197
  29. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/multicor.py +0 -90
  30. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/nx_z_splitter.py +0 -125
  31. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/parse_reconstruction_log.py +0 -151
  32. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/prepare_weights_double.py +0 -163
  33. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/reconstruct.py +0 -120
  34. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/reconstruct_helical.py +0 -116
  35. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/reduce_dark_flat.py +0 -181
  36. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/rotate.py +0 -162
  37. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/shrink_dataset.py +0 -98
  38. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/stitching.py +0 -85
  39. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/tests/test_reduce_dark_flat.py +0 -78
  40. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/utils.py +0 -33
  41. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/validator.py +0 -110
  42. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/__init__.py +0 -0
  43. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/convolution.py +0 -8
  44. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/fft.py +0 -4
  45. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/kernel.py +0 -97
  46. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/medfilt.py +0 -6
  47. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/padding.py +0 -6
  48. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/processing.py +0 -75
  49. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/tests/__init__.py +0 -1
  50. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/utils.py +0 -331
  51. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/__init__.py +0 -12
  52. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/alignment.py +0 -578
  53. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/cor.py +0 -1621
  54. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/cor_sino.py +0 -183
  55. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/distortion.py +0 -112
  56. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/focus.py +0 -362
  57. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/__init__.py +0 -0
  58. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_alignment.py +0 -70
  59. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_cor.py +0 -472
  60. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_focus.py +0 -105
  61. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_tilt.py +0 -41
  62. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_translation.py +0 -78
  63. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tilt.py +0 -214
  64. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/translation.py +0 -193
  65. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/utils.py +0 -39
  66. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/__init__.py +0 -2
  67. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/cast_volume.py +0 -371
  68. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/detector_distortion.py +0 -305
  69. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/reader.py +0 -628
  70. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/reader_helical.py +0 -114
  71. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tests/__init__.py +0 -0
  72. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tests/test_cast_volume.py +0 -339
  73. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tests/test_detector_distortion.py +0 -178
  74. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tests/test_writers.py +0 -187
  75. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tiffwriter_zmm.py +0 -99
  76. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/utils.py +0 -263
  77. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/writer.py +0 -892
  78. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/__init__.py +0 -0
  79. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/binning.py +0 -98
  80. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/fftshift.py +0 -6
  81. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/filters.py +0 -24
  82. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/fourier_filters.py +0 -152
  83. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/histogram.py +0 -6
  84. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/histogram_cuda.py +0 -8
  85. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/kernel_base.py +0 -4
  86. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/padding.py +0 -83
  87. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/padding_base.py +0 -6
  88. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/processing_base.py +0 -4
  89. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/rotation.py +0 -6
  90. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/rotation_cuda.py +0 -6
  91. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/tests/__init__.py +0 -1
  92. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/tests/test_binning.py +0 -48
  93. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/tests/test_interpolation.py +0 -70
  94. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/transpose.py +0 -6
  95. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/unsharp.py +0 -4
  96. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/unsharp_cuda.py +0 -6
  97. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/unsharp_opencl.py +0 -8
  98. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/utils.py +0 -117
  99. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/__init__.py +0 -0
  100. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/fft.py +0 -6
  101. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/kernel.py +0 -135
  102. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/memcpy.py +0 -35
  103. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/padding.py +0 -6
  104. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/processing.py +0 -62
  105. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/tests/__init__.py +0 -0
  106. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/utils.py +0 -292
  107. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/__init__.py +0 -0
  108. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/config.py +0 -265
  109. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/config_validators.py +0 -589
  110. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/datadump.py +0 -164
  111. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/dataset_validator.py +0 -211
  112. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/detector_distortion_provider.py +0 -20
  113. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/estimators.py +0 -1012
  114. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fallback_utils.py +0 -149
  115. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/__init__.py +0 -0
  116. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/chunked.py +0 -849
  117. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/chunked_cuda.py +0 -152
  118. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/computations.py +0 -260
  119. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/dataset_validator.py +0 -63
  120. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/nabu_config.py +0 -590
  121. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/processconfig.py +0 -825
  122. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/reconstruction.py +0 -851
  123. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/__init__.py +0 -0
  124. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/dataset_validator.py +0 -19
  125. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/fbp.py +0 -147
  126. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/filtering.py +0 -246
  127. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/gridded_accumulator.py +0 -575
  128. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_chunked_regridded.py +0 -1670
  129. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_chunked_regridded_cuda.py +0 -119
  130. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_reconstruction.py +0 -598
  131. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_utils.py +0 -42
  132. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/nabu_config.py +0 -175
  133. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/processconfig.py +0 -62
  134. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/span_strategy.py +0 -483
  135. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/__init__.py +0 -0
  136. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/test_accumulator.py +0 -157
  137. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/test_pipeline_elements_full.py +0 -355
  138. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/test_strategy.py +0 -61
  139. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/utils.py +0 -51
  140. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/weight_balancer.py +0 -101
  141. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/params.py +0 -163
  142. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/processconfig.py +0 -210
  143. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/tests/test_chunk_reader.py +0 -78
  144. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/tests/test_estimators.py +0 -149
  145. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/utils.py +0 -116
  146. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/writer.py +0 -193
  147. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/xrdct/__init__.py +0 -0
  148. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/__init__.py +0 -7
  149. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/alignment.py +0 -11
  150. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ccd.py +0 -161
  151. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ccd_cuda.py +0 -169
  152. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ctf.py +0 -361
  153. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ctf_cuda.py +0 -142
  154. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/distortion.py +0 -92
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  1979. build/lib/nabu/preproc/flatfield_cuda.py +0 -144
  1980. build/lib/nabu/preproc/flatfield_variable_region.py +0 -79
  1981. build/lib/nabu/preproc/phase.py +0 -425
  1982. build/lib/nabu/preproc/phase_cuda.py +0 -143
  1983. build/lib/nabu/preproc/shift.py +0 -95
  1984. build/lib/nabu/preproc/shift_cuda.py +0 -102
  1985. build/lib/nabu/preproc/tests/__init__.py +0 -1
  1986. build/lib/nabu/preproc/tests/test_ccd_corr.py +0 -59
  1987. build/lib/nabu/preproc/tests/test_ctf.py +0 -250
  1988. build/lib/nabu/preproc/tests/test_double_flatfield.py +0 -86
  1989. build/lib/nabu/preproc/tests/test_flatfield.py +0 -626
  1990. build/lib/nabu/preproc/tests/test_paganin.py +0 -67
  1991. build/lib/nabu/preproc/tests/test_vshift.py +0 -73
  1992. build/lib/nabu/processing/__init__.py +0 -0
  1993. build/lib/nabu/processing/convolution_cuda.py +0 -375
  1994. build/lib/nabu/processing/fft_base.py +0 -163
  1995. build/lib/nabu/processing/fft_cuda.py +0 -256
  1996. build/lib/nabu/processing/fft_opencl.py +0 -54
  1997. build/lib/nabu/processing/fftshift.py +0 -134
  1998. build/lib/nabu/processing/histogram.py +0 -286
  1999. build/lib/nabu/processing/histogram_cuda.py +0 -103
  2000. build/lib/nabu/processing/kernel_base.py +0 -126
  2001. build/lib/nabu/processing/medfilt_cuda.py +0 -159
  2002. build/lib/nabu/processing/muladd.py +0 -29
  2003. build/lib/nabu/processing/muladd_cuda.py +0 -68
  2004. build/lib/nabu/processing/padding_base.py +0 -71
  2005. build/lib/nabu/processing/padding_cuda.py +0 -75
  2006. build/lib/nabu/processing/padding_opencl.py +0 -77
  2007. build/lib/nabu/processing/processing_base.py +0 -123
  2008. build/lib/nabu/processing/roll_opencl.py +0 -64
  2009. build/lib/nabu/processing/rotation.py +0 -63
  2010. build/lib/nabu/processing/rotation_cuda.py +0 -66
  2011. build/lib/nabu/processing/tests/__init__.py +0 -0
  2012. build/lib/nabu/processing/tests/test_fft.py +0 -268
  2013. build/lib/nabu/processing/tests/test_fftshift.py +0 -71
  2014. build/lib/nabu/processing/tests/test_histogram.py +0 -55
  2015. build/lib/nabu/processing/tests/test_medfilt.py +0 -77
  2016. build/lib/nabu/processing/tests/test_muladd.py +0 -54
  2017. build/lib/nabu/processing/tests/test_padding.py +0 -247
  2018. build/lib/nabu/processing/tests/test_roll.py +0 -63
  2019. build/lib/nabu/processing/tests/test_rotation.py +0 -83
  2020. build/lib/nabu/processing/tests/test_transpose.py +0 -72
  2021. build/lib/nabu/processing/tests/test_unsharp.py +0 -106
  2022. build/lib/nabu/processing/transpose.py +0 -126
  2023. build/lib/nabu/processing/unsharp.py +0 -79
  2024. build/lib/nabu/processing/unsharp_cuda.py +0 -53
  2025. build/lib/nabu/processing/unsharp_opencl.py +0 -75
  2026. build/lib/nabu/reconstruction/__init__.py +0 -3
  2027. build/lib/nabu/reconstruction/cone.py +0 -241
  2028. build/lib/nabu/reconstruction/fbp.py +0 -124
  2029. build/lib/nabu/reconstruction/fbp_base.py +0 -391
  2030. build/lib/nabu/reconstruction/fbp_opencl.py +0 -78
  2031. build/lib/nabu/reconstruction/filtering.py +0 -220
  2032. build/lib/nabu/reconstruction/filtering_cuda.py +0 -103
  2033. build/lib/nabu/reconstruction/filtering_opencl.py +0 -111
  2034. build/lib/nabu/reconstruction/projection.py +0 -240
  2035. build/lib/nabu/reconstruction/reconstructor.py +0 -174
  2036. build/lib/nabu/reconstruction/reconstructor_cuda.py +0 -44
  2037. build/lib/nabu/reconstruction/rings.py +0 -248
  2038. build/lib/nabu/reconstruction/rings_cuda.py +0 -322
  2039. build/lib/nabu/reconstruction/sinogram.py +0 -467
  2040. build/lib/nabu/reconstruction/sinogram_cuda.py +0 -250
  2041. build/lib/nabu/reconstruction/sinogram_opencl.py +0 -40
  2042. build/lib/nabu/reconstruction/tests/__init__.py +0 -1
  2043. build/lib/nabu/reconstruction/tests/test_cone.py +0 -308
  2044. build/lib/nabu/reconstruction/tests/test_deringer.py +0 -220
  2045. build/lib/nabu/reconstruction/tests/test_fbp.py +0 -252
  2046. build/lib/nabu/reconstruction/tests/test_filtering.py +0 -133
  2047. build/lib/nabu/reconstruction/tests/test_halftomo.py +0 -100
  2048. build/lib/nabu/reconstruction/tests/test_projector.py +0 -164
  2049. build/lib/nabu/reconstruction/tests/test_reconstructor.py +0 -93
  2050. build/lib/nabu/reconstruction/tests/test_sino_normalization.py +0 -85
  2051. build/lib/nabu/resources/__init__.py +0 -0
  2052. build/lib/nabu/resources/cli/__init__.py +0 -0
  2053. build/lib/nabu/resources/cor.py +0 -5
  2054. build/lib/nabu/resources/dataset_analyzer.py +0 -469
  2055. build/lib/nabu/resources/gpu.py +0 -169
  2056. build/lib/nabu/resources/logger.py +0 -130
  2057. build/lib/nabu/resources/nxflatfield.py +0 -217
  2058. build/lib/nabu/resources/templates/__init__.py +0 -0
  2059. build/lib/nabu/resources/tests/__init__.py +0 -0
  2060. build/lib/nabu/resources/tests/test_nxflatfield.py +0 -104
  2061. build/lib/nabu/resources/tests/test_units.py +0 -47
  2062. build/lib/nabu/resources/utils.py +0 -174
  2063. build/lib/nabu/stitching/__init__.py +0 -0
  2064. build/lib/nabu/stitching/alignment.py +0 -184
  2065. build/lib/nabu/stitching/config.py +0 -1286
  2066. build/lib/nabu/stitching/definitions.py +0 -6
  2067. build/lib/nabu/stitching/frame_composition.py +0 -155
  2068. build/lib/nabu/stitching/overlap.py +0 -373
  2069. build/lib/nabu/stitching/sample_normalization.py +0 -60
  2070. build/lib/nabu/stitching/slurm_utils.py +0 -204
  2071. build/lib/nabu/stitching/tests/__init__.py +0 -0
  2072. build/lib/nabu/stitching/tests/test_alignment.py +0 -99
  2073. build/lib/nabu/stitching/tests/test_config.py +0 -226
  2074. build/lib/nabu/stitching/tests/test_frame_composition.py +0 -180
  2075. build/lib/nabu/stitching/tests/test_overlap.py +0 -98
  2076. build/lib/nabu/stitching/tests/test_sample_normalization.py +0 -49
  2077. build/lib/nabu/stitching/tests/test_slurm_utils.py +0 -146
  2078. build/lib/nabu/stitching/tests/test_utils.py +0 -21
  2079. build/lib/nabu/stitching/tests/test_z_stitching.py +0 -1183
  2080. build/lib/nabu/stitching/utils.py +0 -563
  2081. build/lib/nabu/stitching/z_stitching.py +0 -2279
  2082. build/lib/nabu/tests.py +0 -51
  2083. build/lib/nabu/testutils.py +0 -375
  2084. build/lib/nabu/thirdparty/__init__.py +0 -0
  2085. build/lib/nabu/thirdparty/algotom_convert_sino.py +0 -276
  2086. build/lib/nabu/thirdparty/pore3d_deringer_munch.py +0 -108
  2087. build/lib/nabu/thirdparty/tomocupy_remove_stripe.py +0 -586
  2088. build/lib/nabu/thirdparty/tomopy_phase.py +0 -239
  2089. build/lib/nabu/thirdparty/tomwer_load_flats_darks.py +0 -162
  2090. build/lib/nabu/utils.py +0 -836
  2091. nabu-2024.1.1.dist-info/RECORD +0 -2375
  2092. nabu-2024.1.1.dist-info/top_level.txt +0 -4
  2093. {build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app → nabu/app/tests}/__init__.py +0 -0
  2094. {nabu-2024.1.1.dist-info → nabu-2024.1.2.dist-info}/LICENSE +0 -0
  2095. {nabu-2024.1.1.dist-info → nabu-2024.1.2.dist-info}/entry_points.txt +0 -0
@@ -1,575 +0,0 @@
1
- from ...preproc.flatfield import FlatFieldArrays
2
- import numpy as np
3
- from scipy import ndimage as nd
4
- import math
5
-
6
-
7
- class GriddedAccumulator:
8
- nominal_current = 0.2
9
-
10
- def __init__(
11
- self,
12
- gridded_radios,
13
- gridded_weights,
14
- diagnostic_radios,
15
- diagnostic_weights,
16
- diagnostic_angles,
17
- diagnostic_searched_angles_rad_clipped,
18
- diagnostic_zpix_transl,
19
- diag_zpro_run=0,
20
- dark=None,
21
- flat_indexes=None,
22
- flats=None,
23
- weights=None,
24
- double_flat=None,
25
- radios_srcurrent=None,
26
- flats_srcurrent=None,
27
- ):
28
- """
29
- This class creates, for a selected volume slab, a standard set of radios from an helical dataset.
30
-
31
- Parameters
32
- ==========
33
-
34
- gridded_radios : 3D np.array
35
- this is the stack of new radios which will be resynthetised, by this class,
36
- for a selected slab.
37
- The object is initialised with this array, and this array will accumulate, during subsequent
38
- calls to method extract_preprocess_with_flats, the sum of the transformed contributions
39
- obtained from the arguments of the mentioned method (extract_preprocess_with_flats).
40
- gridded_weights : 3d np.array
41
- same shape as gridded_radios, but it will accumulate the weights, during calls to
42
- extract_preprocess_with_flats
43
- diag_zpro_run: int
44
- if > 0 then only the diagnostics are filled, and no accumulation is done
45
-
46
- diagnostic_searched_angles_rad_clipped:
47
- the angles between 0 and 2pi. The contributions to diagnostic will be searched for these angles
48
- plus for the same angles + 2pi ( following turn)
49
-
50
- diagnostic_radios : 3d np.array, a stack composed of
51
- each radio must have the same size as a radio of the gridded_radios argument.
52
- During the calls to extract_preprocess_with_flats methods,
53
- the radios will collect the transformed data for the angles given by diagnostic_searched_angles_rad_clipped and redundancy
54
- diagnostic_weights: 3d np.array a stack composed of two radios
55
- Same shape as diagnostic_radios. The weigths for diagnostic radios ( will be zero on pixel
56
- where no data is available, or where the weight is null)
57
- diagnostic_angles : 1D np.array
58
- Must have shape==(2*len(diagnostic_searched_angles_rad_clipped),). The entries will be filled with the angles at which the contributions
59
- to diagnostic_radios have been summed.
60
- diagnostic_zpix_transl: 1D np.array
61
- same as for diagnostic_angles, but for vertical translation in pixels
62
- dark: None or 2D np.array
63
- must have the shape of the detector ( generally larger that a radio of gridded_radios)
64
- If given, the dark will be subtracted from data and flats.
65
- radios_srcurrent: 1D np.array
66
- the machine current for every radio
67
- flats_srcurrent: 1D np.array
68
- the machine current for every flat
69
-
70
-
71
- flat_indexes: None or a list of integers
72
- the projection index corresponding to the flats
73
- flats : None or 3D np.array
74
- the stack of flats. Each flat must have the shape of the detector (generally larger that a radio of gridded_radios)
75
- The flats, if given, are subtracted of the dark, if given, and the result is used to normalise the data.
76
- weights : None or 2D np.array
77
- If not given each data pixel will be considered with unit weight.
78
- If given it must have the same shape as the detector.
79
- double_flat = None or 2D np.array
80
- If given, the double flat will be applied (division by double_flat)
81
- Must have the same shape as the detector.
82
- """
83
- self.diag_zpro_run = diag_zpro_run
84
- self.gridded_radios = gridded_radios
85
- self.gridded_weights = gridded_weights
86
- self.diagnostic_radios = diagnostic_radios
87
- self.diagnostic_weights = diagnostic_weights
88
- self.diagnostic_angles = diagnostic_angles
89
-
90
- self.diagnostic_zpix_transl = diagnostic_zpix_transl
91
- self.diagnostic_searched_angles_rad_clipped = diagnostic_searched_angles_rad_clipped
92
-
93
- self.dark = dark
94
-
95
- self.radios_srcurrent = radios_srcurrent
96
-
97
- self.flats_srcurrent = flats_srcurrent
98
-
99
- self.flat_indexes = flat_indexes
100
- self.flat_indexes_reverse_map = dict(
101
- [(global_index, local_index) for (local_index, global_index) in enumerate(flat_indexes)]
102
- )
103
- self.flats = flats
104
- self.weights = weights
105
- self.double_flat = double_flat
106
-
107
- def extract_preprocess_with_flats(
108
- self,
109
- subchunk_slice,
110
- subchunk_file_indexes,
111
- chunk_info,
112
- subr_start_end,
113
- dtasrc_start_end,
114
- data_raw,
115
- radios_angular_range_slicing,
116
- ):
117
- """
118
- This functions is meant to be called providing, each time, a subset of the data
119
- which are needed to reconstruct a chunk (to reconstruct a slab).
120
- When all the necessary data have flown through the subsequent calls to this method,
121
- the accumulators are ready.
122
-
123
- Parameters
124
- ==========
125
- subchunk_slice: an object of the python class "slice"
126
- this slice slices the angular domain which corresponds to the useful
127
- projections which are useful for the chunk, and whose informations
128
- are contained in the companion argument "chunk_info"
129
- Such slicing correspond to the angular subset, for which we are providing
130
- data_raw
131
- subchunk_file_indexes: a sequence of integers.
132
- they correspond to the projection numbers from which the data in data_raw are coming.
133
- They are used to interpolate between falt fields
134
- chunk_info: an object returned by the get_chunk_info of the SpanStrategy class
135
- this object must have the following members, which relates to the wanted chunk
136
-
137
- angle_index_span: a pair of integers indicating the start and the end of useful angles
138
- in the array of all the scan angle self.projection_angles_deg
139
- span_v: a pair of two integers indicating the start and end of the span relatively to the lowest value
140
- of array self.total_view_heights
141
- integer_shift_v: an array, containing for each one of the useful projections of the span,
142
- the integer part of vertical shift to be used in cropping,
143
- fract_complement_to_integer_shift_v :
144
- the fractional remainder for cropping.
145
- z_pix_per_proj: an array, containing for each to be used projection of the span
146
- the vertical shift
147
- x_pix_per_proj: ....the horizontal shift
148
- angles_rad : an array, for each useful projection of the chunk the angle in radian
149
- subr_start_end: a pair of integers
150
- the start height, and the end height, of the slab for which we are collecting the data.
151
- The number are given with the same logic as for member span_v of the chunk_info.
152
- Without the phase margin, when the phase margin is zero, hey would correspond exactly to
153
- the start and end, vertically, of the reconstructed slices.
154
- dtasrc_start_end: a pair of integers
155
- This number are relative to the detector ( they are detector line indexes).
156
- They indicated, vertically, the detector portion the data_raw data correspond to
157
- data_raw: np.array 3D
158
- the data which correspond to a limited detector stripe and a limited angular subset
159
- radios_angular_range_slicing:
160
- my_subsampled_indexes is important in order to compare the
161
- radios positions with respect to the flat position, and these position
162
- are given as the sequential acquisition number which counts everything ( flats, darks, radios )
163
- Insteqd, in order to access array which spans only the radios, we need to have an idea of where we are.
164
- this is provided by radios_angular_range_slicing which addresses the radios domain
165
-
166
- """
167
-
168
- # the object below is going to containing some auxiliary variable that are use to reframe the data.
169
- # This object is used to pass in a compact way such informations to different methods.
170
- # The informations are extracted from chunk info
171
- reframing_infos = self._ReframingInfos(
172
- chunk_info, subchunk_slice, subr_start_end, dtasrc_start_end, subchunk_file_indexes
173
- )
174
-
175
- # give the proper dimensioning to an auxiliary stack which will contain the reframed data extracted
176
- # from the treatement of the sub-chunk
177
- radios_subset = np.zeros(
178
- [data_raw.shape[0], subr_start_end[1] - subr_start_end[0], data_raw.shape[2]], np.float32
179
- )
180
-
181
- # ... and in the same way we dimension the container for the associated reframed weights.
182
- radios_weights_subset = np.zeros(
183
- [data_raw.shape[0], subr_start_end[1] - subr_start_end[0], data_raw.shape[2]], np.float32
184
- )
185
-
186
- # extraction of the data
187
- self._extract_preprocess_with_flats(
188
- data_raw, reframing_infos, chunk_info, radios_subset, radios_angular_range_slicing
189
- )
190
-
191
- if self.weights is not None:
192
- # ... and, if required, extraction of the associated weights
193
- wdata_read = self.weights.data[reframing_infos.dtasrc_start_z : reframing_infos.dtasrc_end_z]
194
- self._extract_preprocess_with_flats(
195
- wdata_read, reframing_infos, chunk_info, radios_weights_subset, it_is_weight=True
196
- )
197
-
198
- else:
199
- radios_weights_subset[:] = 1.0
200
-
201
- # and the remaining part is a simple projection over the accumulators, for
202
- # the data and for the weights
203
- my_angles = chunk_info.angles_rad[subchunk_slice]
204
-
205
- n_gridded_angles = self.gridded_radios.shape[0]
206
-
207
- my_i_float = my_angles * (n_gridded_angles / (2 * math.pi))
208
-
209
- tmp_i_rounded = np.floor(my_i_float).astype(np.int32)
210
- my_epsilon = my_i_float - tmp_i_rounded
211
- my_i0 = np.mod(tmp_i_rounded, n_gridded_angles)
212
- my_i1 = np.mod(my_i0 + 1, n_gridded_angles)
213
-
214
- if self.diag_zpro_run:
215
- # these are used only when collection the diagnostics
216
-
217
- # an estimation of the angular step
218
- my_angle_step_rad = abs(np.diff(chunk_info.angles_rad[subchunk_slice]).mean())
219
- my_angles_02pi = np.mod(my_angles, 2 * np.pi)
220
- # bins are delimited by ticks
221
- ticks = np.empty(2 * len(self.diagnostic_searched_angles_rad_clipped), "f")
222
- ticks[::2] = self.diagnostic_searched_angles_rad_clipped - my_angle_step_rad / 2
223
- ticks[1::2] = ticks[::2] + my_angle_step_rad
224
-
225
- for i0, epsilon, i1, data, weight, original_angle, original_zpix_transl in zip(
226
- my_i0,
227
- my_epsilon,
228
- my_i1,
229
- radios_subset,
230
- radios_weights_subset,
231
- chunk_info.angles_rad[subchunk_slice],
232
- chunk_info.z_pix_per_proj[subchunk_slice],
233
- ):
234
- data_token = data * weight
235
-
236
- if not self.diag_zpro_run:
237
- self.gridded_radios[i0] += data_token * (1 - epsilon)
238
- self.gridded_radios[i1] += data_token * epsilon
239
-
240
- self.gridded_weights[i0] += weight * (1 - epsilon)
241
- self.gridded_weights[i1] += weight * epsilon
242
-
243
- # building the intervals around the diagnostic angles
244
-
245
- if self.diag_zpro_run:
246
- my_i0 = np.searchsorted(ticks, my_angles_02pi)
247
-
248
- for i0, a02pi, data, weight, original_angle, original_zpix_transl in zip(
249
- my_i0,
250
- my_angles_02pi,
251
- radios_subset,
252
- radios_weights_subset,
253
- chunk_info.angles_rad[subchunk_slice],
254
- chunk_info.z_pix_per_proj[subchunk_slice],
255
- ):
256
- if i0 % 2 == 0:
257
- # not in an intervals
258
- continue
259
-
260
- # There is a contribution to the first regridded radio ( the one indexed by 0)
261
- # We build two diagnostics for the contributions to this radio.
262
- # The first for the first pass (i_diag=0)
263
- # The second for the second pass if any (i_diag=1)
264
-
265
- # To discriminate we introduce
266
- # An angular margin beyond which we know that a possible contribution
267
- # is coming from another turn
268
-
269
- safe_angular_margin = 3.14 / 40
270
-
271
- my_dist = abs(
272
- a02pi - self.diagnostic_searched_angles_rad_clipped[(i0 - 1) // 2 : (i0 - 1) // 2 + 1].mean()
273
- )
274
-
275
- # print(" i0 ", i0, " original_angle ", original_angle, " a02pi" , a02pi, " my_dist " , my_dist)
276
-
277
- # consider fist pass and second possible pass. There might be further passes which we dont consider here
278
- i_diag_list = [(i0 - 1) // 2, (i0 - 1) // 2 + len(self.diagnostic_searched_angles_rad_clipped)]
279
- for i_redundancy, i_diag in enumerate(i_diag_list):
280
- # print("IRED ", i_redundancy)
281
- if i_redundancy:
282
- # to avoid, in z_stages with >360 range for one single stage, to fill the second items which should instead be filled by another stage.
283
- if abs(original_zpix_transl - self.diagnostic_zpix_transl[i_diag_list[0]]) < 2.0:
284
- # print( " >>>>>> stesso z" , i_redundancy )
285
- continue
286
-
287
- if np.isnan(self.diagnostic_angles[i_diag]) or (
288
- abs(original_angle) < abs(self.diagnostic_angles[i_diag] + safe_angular_margin)
289
- ):
290
- # we are searching for the first contributions ( the one at the lowest angle)
291
- # for the two diagnostics. With the constraint that the second is at an higher angle
292
- # than the first. So if we are here this means that we have found an occurrence with
293
- # lower angle and we discard what we could have previously found.
294
-
295
- self.diagnostic_radios[i_diag][:] = 0
296
- self.diagnostic_weights[i_diag][:] = 0
297
- self.diagnostic_angles[i_diag] = original_angle
298
-
299
- self.diagnostic_zpix_transl[i_diag] = original_zpix_transl
300
- else:
301
- continue
302
-
303
- if abs(my_dist) <= my_angle_step_rad * 1.1:
304
- factor = 1 - abs(my_dist) / (my_angle_step_rad)
305
-
306
- self.diagnostic_radios[i_diag] += data_token * factor
307
- self.diagnostic_weights[i_diag] += weight * factor
308
- break
309
- else:
310
- pass
311
-
312
- class _ReframingInfos:
313
- def __init__(self, chunk_info, subchunk_slice, subr_start_end, dtasrc_start_end, subchunk_file_indexes):
314
- self.subchunk_file_indexes = subchunk_file_indexes
315
- my_integer_shifts_v = chunk_info.integer_shift_v[subchunk_slice]
316
- self.fract_complement_shifts_v = chunk_info.fract_complement_to_integer_shift_v[subchunk_slice]
317
- self.x_shifts_list = chunk_info.x_pix_per_proj[subchunk_slice]
318
- subr_start_z, subr_end_z = subr_start_end
319
- self.subr_start_z_list = subr_start_z - my_integer_shifts_v
320
- self.subr_end_z_list = subr_end_z - my_integer_shifts_v + 1
321
-
322
- self.dtasrc_start_z, self.dtasrc_end_z = dtasrc_start_end
323
-
324
- floating_start_z = self.subr_start_z_list.min()
325
- floating_end_z = self.subr_end_z_list.max()
326
-
327
- self.floating_subregion = None, None, floating_start_z, floating_end_z
328
-
329
- def _extract_preprocess_with_flats(
330
- self, data_raw, reframing_infos, chunk_info, output, radios_angular_range_slicing=None, it_is_weight=False
331
- ):
332
- if not it_is_weight:
333
- if self.dark is not None:
334
- data_raw = data_raw - self.dark[reframing_infos.dtasrc_start_z : reframing_infos.dtasrc_end_z]
335
-
336
- if self.flats is not None:
337
- for i, idx in enumerate(reframing_infos.subchunk_file_indexes):
338
- flat = self._get_flat(idx, slice(reframing_infos.dtasrc_start_z, reframing_infos.dtasrc_end_z))
339
- if self.dark is not None:
340
- flat = flat - self.dark[reframing_infos.dtasrc_start_z : reframing_infos.dtasrc_end_z]
341
-
342
- if self.radios_srcurrent is not None:
343
- factor = self.nominal_current / self.radios_srcurrent[radios_angular_range_slicing.start + i]
344
- else:
345
- factor = 1
346
-
347
- data_raw[i] = data_raw[i] * factor / flat
348
-
349
- if self.double_flat is not None:
350
- data_raw = data_raw / self.double_flat[reframing_infos.dtasrc_start_z : reframing_infos.dtasrc_end_z]
351
-
352
- if it_is_weight:
353
- # for the weight, the detector weights, depends on the detector portion,
354
- # the one corresponding to dtasrc_start_end, and is the same across
355
- # the subchunk first index ( the projection index)
356
- take_data_from_this = [data_raw] * len(reframing_infos.subr_start_z_list)
357
- else:
358
- take_data_from_this = data_raw
359
-
360
- for data_read, list_subr_start_z, list_subr_end_z, fract_shift, x_shift, data_target in zip(
361
- take_data_from_this,
362
- reframing_infos.subr_start_z_list,
363
- reframing_infos.subr_end_z_list,
364
- reframing_infos.fract_complement_shifts_v,
365
- reframing_infos.x_shifts_list,
366
- output,
367
- ):
368
- _fill_in_chunk_by_shift_crop_data(
369
- data_target,
370
- data_read,
371
- fract_shift,
372
- list_subr_start_z,
373
- list_subr_end_z,
374
- reframing_infos.dtasrc_start_z,
375
- reframing_infos.dtasrc_end_z,
376
- x_shift=x_shift,
377
- extension_padding=(not it_is_weight),
378
- )
379
-
380
- def _get_flat(self, idx, slice_y=slice(None, None), slice_x=slice(None, None), dtype=np.float32):
381
- prev_next = FlatFieldArrays.get_previous_next_indices(self.flat_indexes, idx)
382
-
383
- if len(prev_next) == 1: # current index corresponds to an acquired flat
384
- flat_data = self.flats[self.flat_indexes_reverse_map[prev_next[0]]][slice_y, slice_x]
385
- else: # interpolate
386
- prev_idx, next_idx = prev_next
387
-
388
- n_prev = self.flat_indexes_reverse_map[prev_idx]
389
- n_next = self.flat_indexes_reverse_map[next_idx]
390
-
391
- flat_data_prev = self.flats[n_prev][slice_y, slice_x]
392
- flat_data_next = self.flats[n_next][slice_y, slice_x]
393
-
394
- if self.flats_srcurrent is not None:
395
- prev_current_factor = self.nominal_current / self.flats_srcurrent[n_prev]
396
- next_current_factor = self.nominal_current / self.flats_srcurrent[n_next]
397
- else:
398
- prev_current_factor = 1
399
- next_current_factor = 1
400
-
401
- delta = next_idx - prev_idx
402
- w1 = 1 - (idx - prev_idx) / delta
403
- w2 = 1 - (next_idx - idx) / delta
404
-
405
- if self.dark is not None:
406
- dark = self.dark[slice_y, slice_x]
407
- else:
408
- dark = 0
409
-
410
- flat_data = (
411
- dark
412
- + w1 * (flat_data_prev - dark) * prev_current_factor
413
- + w2 * (flat_data_next - dark) * next_current_factor
414
- )
415
-
416
- if flat_data.dtype != dtype:
417
- flat_data = np.ascontiguousarray(flat_data, dtype=dtype)
418
- return flat_data
419
-
420
-
421
- def _fill_in_chunk_by_shift_crop_data(
422
- data_target,
423
- data_read,
424
- fract_shift,
425
- my_subr_start_z,
426
- my_subr_end_z,
427
- dtasrc_start_z,
428
- dtasrc_end_z,
429
- x_shift=0.0,
430
- extension_padding=True,
431
- ):
432
- data_read_precisely_shifted = nd.shift(data_read, (-fract_shift, x_shift), order=1, mode="nearest")[:-1]
433
-
434
- target_central_slicer, dtasrc_central_slicer = overlap_logic(
435
- my_subr_start_z, my_subr_end_z - 1, dtasrc_start_z, dtasrc_end_z - 1
436
- )
437
-
438
- if None not in [target_central_slicer, dtasrc_central_slicer]:
439
- data_target[target_central_slicer] = data_read_precisely_shifted[dtasrc_central_slicer]
440
-
441
- target_lower_slicer, target_upper_slicer = padding_logic(
442
- my_subr_start_z, my_subr_end_z - 1, dtasrc_start_z, dtasrc_end_z - 1
443
- )
444
-
445
- if extension_padding:
446
- if target_lower_slicer is not None:
447
- data_target[target_lower_slicer] = data_read_precisely_shifted[0]
448
- if target_upper_slicer is not None:
449
- data_target[target_upper_slicer] = data_read_precisely_shifted[-1]
450
- else:
451
- if target_lower_slicer is not None:
452
- data_target[target_lower_slicer] = 1.0e-6
453
- if target_upper_slicer is not None:
454
- data_target[target_upper_slicer] = 1.0e-6
455
-
456
-
457
- def overlap_logic(subr_start_z, subr_end_z, dtasrc_start_z, dtasrc_end_z):
458
- """determines the useful lines which can be transferred from the dtasrc_start_z:dtasrc_end_z
459
- range targeting the range subr_start_z: subr_end_z ..................
460
-
461
- """
462
-
463
- t_h = subr_end_z - subr_start_z
464
- s_h = dtasrc_end_z - dtasrc_start_z
465
-
466
- my_start = max(0, dtasrc_start_z - subr_start_z)
467
- my_end = min(t_h, dtasrc_end_z - subr_start_z)
468
-
469
- if my_start >= my_end:
470
- return None, None
471
-
472
- target_central_slicer = slice(my_start, my_end)
473
-
474
- my_start = max(0, subr_start_z - dtasrc_start_z)
475
- my_end = min(s_h, subr_end_z - dtasrc_start_z)
476
-
477
- assert my_start < my_end, "Overlap_logic logic error"
478
-
479
- dtasrc_central_slicer = slice(my_start, my_end)
480
-
481
- return target_central_slicer, dtasrc_central_slicer
482
-
483
-
484
- def padding_logic(subr_start_z, subr_end_z, dtasrc_start_z, dtasrc_end_z):
485
- """.......... and the missing ranges which possibly could be obtained by extension padding"""
486
- t_h = subr_end_z - subr_start_z
487
- s_h = dtasrc_end_z - dtasrc_start_z
488
-
489
- if dtasrc_start_z <= subr_start_z:
490
- target_lower_padding = None
491
- else:
492
- target_lower_padding = slice(0, dtasrc_start_z - subr_start_z)
493
-
494
- if dtasrc_end_z >= subr_end_z:
495
- target_upper_padding = None
496
- else:
497
- target_upper_padding = slice(dtasrc_end_z - subr_end_z, None)
498
-
499
- return target_lower_padding, target_upper_padding
500
-
501
-
502
- def get_reconstruction_space(span_info, min_scanwise_z, end_scanwise_z, phase_margin_pix):
503
- """Utility function, so far used only by the unit test, which, given the span_info object, creates the auxiliary collection arrays
504
- and initialises the my_z_min, my_z_end variable keeping into account the scan direction
505
- and the min_scanwise_z, end_scanwise_z input arguments
506
- Parameters
507
- ==========
508
-
509
- span_info: SpanStrategy
510
-
511
- min_scanwise_z: int
512
- non negative number, where zero indicates the first feaseable slice doable scanwise.
513
- Indicates the first (scanwise) requested slice to be reconstructed
514
-
515
- end_scanwise_z: int
516
- non negative number, where zero indicates the first feaseable slice doable scanwise.
517
- Indicates the end (scanwise) slice which delimity the to be reconstructed requested slab.
518
-
519
- """
520
-
521
- detector_z_start, detector_z_end = (span_info.get_doable_span()).view_heights_minmax
522
-
523
- if span_info.z_pix_per_proj[-1] > span_info.z_pix_per_proj[0]:
524
- my_z_min = detector_z_start + min_scanwise_z
525
- my_z_end = detector_z_start + end_scanwise_z
526
- else:
527
- my_z_min = detector_z_end - (end_scanwise_z - 1)
528
- my_z_end = detector_z_end - (min_scanwise_z + 1)
529
-
530
- # while the raw dataset may have non uniform angular step
531
- # the regridded dataset will have a constant step.
532
- # We evaluate here below the number of angles for the
533
- # regridded dataset, estimating a meaningul angular step representative
534
- # of the raw data
535
- my_angle_step = abs(np.diff(span_info.projection_angles_deg).mean())
536
- n_gridded_angles = int(round(360.0 / my_angle_step))
537
-
538
- radios_h = phase_margin_pix + (my_z_end - my_z_min) + phase_margin_pix
539
-
540
- # the accumulators
541
- gridded_radios = np.zeros([n_gridded_angles, radios_h, span_info.detector_shape_vh[1]], np.float32)
542
- gridded_cumulated_weights = np.zeros([n_gridded_angles, radios_h, span_info.detector_shape_vh[1]], np.float32)
543
-
544
- # this utility function is meant for testing the reconstruction only, not the diagnostic collection.
545
- # However we build diagnostic targets all the same to feed something through the API
546
- # which contemplates the diagnostics. So that the unit test runs correctly
547
-
548
- diagnostic_radios = np.zeros((4,) + gridded_radios.shape[1:], np.float32)
549
- diagnostic_weights = np.zeros((4,) + gridded_radios.shape[1:], np.float32)
550
- diagnostic_proj_angle = np.zeros([4], "f")
551
-
552
- diagnostic_searched_angles_rad_clipped = (0.5 + np.arange(2)) * (2 * np.pi / (2))
553
- diagnostic_zpix_transl = np.zeros([4], "f")
554
-
555
- gridded_angles_rad = np.arange(n_gridded_angles) * 2 * np.pi / n_gridded_angles
556
- gridded_angles_deg = np.rad2deg(gridded_angles_rad)
557
-
558
- res = type(
559
- "on_the_fly_class_for_reconstruction_room_in_gridded_accumulator.py",
560
- (object,),
561
- {
562
- "my_z_min": my_z_min,
563
- "my_z_end": my_z_end,
564
- "gridded_radios": gridded_radios,
565
- "gridded_cumulated_weights": gridded_cumulated_weights,
566
- "diagnostic_radios": diagnostic_radios,
567
- "diagnostic_weights": diagnostic_weights,
568
- "diagnostic_proj_angle": diagnostic_proj_angle,
569
- "diagnostic_searched_angles_rad_clipped": diagnostic_searched_angles_rad_clipped,
570
- "diagnostic_zpix_transl": diagnostic_zpix_transl,
571
- "gridded_angles_rad": gridded_angles_rad,
572
- "gridded_angles_deg": gridded_angles_deg,
573
- },
574
- )
575
- return res