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
@@ -1,483 +0,0 @@
1
- import math
2
- import numpy as np
3
- from ...resources.logger import LoggerOrPrint
4
- from ...utils import DictToObj
5
-
6
-
7
- class SpanStrategy:
8
- def __init__(
9
- self,
10
- z_pix_per_proj,
11
- x_pix_per_proj,
12
- detector_shape_vh,
13
- phase_margin_pix,
14
- projection_angles_deg,
15
- require_redundancy=False,
16
- pixel_size_mm=0.1,
17
- z_offset_mm=0.0,
18
- logger=None,
19
- angular_tolerance_steps=0.0,
20
- ):
21
- """
22
- This class does all the accounting for the reconstructible slices, giving for each one the list of the useful angles,
23
- of the vertical and horizontal shifts,and more ...
24
-
25
- Parameters
26
- ----------
27
- z_pix_per_proj : array of floats
28
- an array of floats with one entry per projection, in pixel units. The values are the vertical displacements of the detector.
29
- An decreasing z means that the rotation axis is following the positive direction of the detector vertical axis, which is pointing toward the ground.
30
- In the experimental setup, the vertical detector axis is pointing toward the ground. Moreover the values are offsetted so that the
31
- first value is zero. The offset value, in millimiters is z_offset_mm and it is the vertical position of the sample stage relatively
32
- to the center of the detector. A negative z_offset_mm means that the sample stage is below the detector for the first projection, and this is almost
33
- always the case, because the sample is above the sample stage.
34
- A z_pix=0 value indicates that the translation-rotation stage "ground" is exactly at the beam height ( supposed to be near the central line of the detector)
35
- plus z_offset_mm.
36
- A positive z_pix means that the translation stage has been lowered, compared to the first projection, in order to scan higher parts of the sample.
37
- ( the sample is above the translation-rotation stage).
38
- x_pix_per_proj : array of floats
39
- one entry per projection. The horizontal displacement of the detector respect to the rotation axis.
40
- A positive x means that the sample shadow on the detector is moving toward the left of the detector.
41
- (the detector is going right)
42
- detector_shape_vh : a tuple of two ints
43
- the vertical and horizontal dimensions
44
- phase_margin_pix : int
45
- the maximum margin needed for the different kernels (phase, unsharp..) otherwhere in the pipeline
46
- projection_angles_deg : array of floats
47
- per each projection the rotation angle of the sample in degree.
48
- require_redundancy: bool, optional, defaults to False
49
- It can be set to True, when there are dead zones in the detector.
50
- In this case the minimal required angular span is increased from 360 to 2*360
51
- in order to enforce the necessary redundancy, which allows the
52
- correction of the dead zones. The lines which do not satisfy this requirement are not doable.
53
- z_offset_mm: float
54
- the vertical position of the sample stage relatively to the center of the detector. A negative z_offset_mm means that the
55
- sample stage is below the detector for the first projection, and this is almost
56
- always the case, because the sample is above the sample stage.
57
- pixel_size_mm: float, the pixel size in millimiters
58
- this value is used to give results in units of " millimeters above the sample stage"
59
- Althougth internally all is calculated in pixel units, it is useful to incorporate
60
- such information in the spanstrategy object which will then be able to setup
61
- reconstruction informations according to several request formats: be they in
62
- sequential number of reconstructible slices, or millimeters above the stage.
63
- angular_tolerance_steps: float, defaults to zero
64
- the angular tolerance, an angular width expressed in units of an angular step, which is tolerated in
65
- the criteria for deciding if a slice is reconstructable or not
66
- logger : a logger, optional
67
- """
68
- self.logger = LoggerOrPrint(logger)
69
- self.require_redundancy = require_redundancy
70
- self.z_pix_per_proj = z_pix_per_proj
71
- self.x_pix_per_proj = x_pix_per_proj
72
- self.detector_shape_vh = detector_shape_vh
73
- self.total_num_images = len(self.z_pix_per_proj)
74
- self.phase_margin_pix = phase_margin_pix
75
- self.pix_size_mm = pixel_size_mm
76
- self.z_offset_mm = z_offset_mm
77
- self.angular_tolerance_steps = angular_tolerance_steps
78
-
79
- # internally we use increasing angles, so that in all inequalities, that are used
80
- # to check the span, only such case has to be contemplated.
81
- # To do so, if needed, we change the sign of the angles.
82
- if projection_angles_deg[-1] > projection_angles_deg[0]:
83
- self.projection_angles_deg_internally = projection_angles_deg
84
- self.angles_are_inverted = False
85
- else:
86
- self.projection_angles_deg_internally = -projection_angles_deg
87
- self.angles_are_inverted = True
88
- self.projection_angles_deg = projection_angles_deg
89
-
90
- if (
91
- len(self.x_pix_per_proj) != self.total_num_images
92
- or len(self.projection_angles_deg_internally) != self.total_num_images
93
- ):
94
- message = f"""
95
- all the arguments z_pix_per_proj, x_pix_per_proj and projection_angles_deg
96
- must have the same lenght but their lenght were
97
- {len(self.z_pix_per_proj) }, {len(self.x_pix_per_proj) }, {len(self.projection_angles_deg_internally) } respectively """
98
-
99
- raise ValueError(message)
100
-
101
- ## informations to be built are initialised to None here below
102
- """ For a given slice, the procedure for obtaining the useful angles, is based on the "sunshine" image,
103
- The sunshine image has two dimensions, the second one is the projection number
104
- while the first runs over the heights of the slices.
105
- All the logic is based on this image: when a given pixel of this image is zero, this corresponds
106
- to a pair (height,projection) for which there is no contribution of that projection to that slice.
107
- """
108
- self.sunshine_image = None
109
-
110
- """ This will be an array of integer heights. We use a one-to-one correspondance beween these integers and slices
111
- in the reconstructed volume.
112
-
113
- The value of a given item is the vertical coordinate of an horizontal line in in the dectector
114
- (or above or below (negative values) ). More precisely the line over which the corresponding slice gets projected
115
- at the beginning of the scan ( in other words
116
- for the first vertical translation entry of the z_pix_per_proj argument)
117
- Illustratively, a view height equal to zero corresponds to
118
- a slice which projects on row 0 when translation is given by the first value in self.z_pix_per_proj.
119
- Negative integers for the heights are possible too, according to the direction of translations, which may bring
120
- above or below the detector. ( Illustratively
121
- the values in z_pix_per_proj are alway positive for the simple fact that the sample is above
122
- the roto-translation stage and the stage must be lowered in height for the beam to hit the sample.
123
- A scan starts always from a positive z_pix translation but the z_pix value may either decrease
124
- or increase. In fact for practical reasons, after having done a scan in one direction it is convenient to scan
125
- also while coming back after a previous scan)
126
- """
127
- self.total_view_heights = None
128
-
129
- """ A list wich will contain for every reconstructable heigth, listed in self.total_view_heights, and in the same order,
130
- a pair of two integer, the first is the first sequential number of the projection for which the height is projected
131
- inside the detector, the second integer is the last projection number for which the projection occurs inside the detector.
132
- """
133
- self.on_detector_projection_intervals = None
134
-
135
- """ All like self.on_detector_projection_intervals, but considering also the margins (phase, unsharp, etc).
136
- so that the height is projected inside the detector but while keeping
137
- a safe phase_margin_pix distance from the upper and lower border of the detector.
138
- """
139
- self.within_margin_projection_intervals = None
140
-
141
- """ This will contain projection number i_pro, the integer value given by
142
- ceil(z_pix_per_proj[i_pro])
143
- This array, together with the here below array self.fract_complement_to_integer_shift_v
144
- will be used for cropping when the data are collected for a given to be reconstructed chunk.
145
- """
146
- self.integer_shift_v = np.zeros([self.total_num_images], "i")
147
-
148
- """ The fractional vertical shifts are positive floats < 1.0 pixels.
149
- This is the fractional part which, added to self.integer_shift_v,
150
- gives back z_pix_per_proj.
151
- Together with integer_shift_v, this array is meant to be used, by other modules, for cropping
152
- when the data are collected for a given to be reconstructed chunk."""
153
- self.fract_complement_to_integer_shift_v = np.zeros([self.total_num_images], "f")
154
-
155
- self._setup_ephemerides()
156
-
157
- self._setup_sunshine()
158
-
159
- def get_doable_span(self):
160
- """return an object with two properties:
161
- view_heights_minmax: containining minimum and maximum doable height ( detector reference at iproj=0)
162
- z_pix_minmax : containing minimum and maximum heights above the roto-translational sample stage
163
- """
164
- vertical_profile = self.sunshine_image.sum(axis=1)
165
-
166
- doable_indexes = np.arange(len(vertical_profile))[vertical_profile > 0]
167
- vertical_span = doable_indexes.min(), doable_indexes.max()
168
-
169
- if not (vertical_profile[vertical_span[0] : vertical_span[1] + 1] > 0).all():
170
- message = """ Something wrong occurred in the span preprocessing.
171
- It appears that some intermetiade slices are not doables.
172
- The doable span should instead be contiguous. Please signal the problem"""
173
- raise RuntimeError(message)
174
-
175
- view_heights_minmax = self.total_view_heights[list(vertical_span)]
176
-
177
- hmin, hmax = view_heights_minmax
178
- d_v, d_h = self.detector_shape_vh
179
- z_min, z_max = (-self.z_pix_per_proj[0] + (d_v - 1) / 2 - hmax, -self.z_pix_per_proj[0] + (d_v - 1) / 2 - hmin)
180
- res = {
181
- "view_heights_minmax": view_heights_minmax,
182
- "z_pix_minmax": (z_min, z_max),
183
- "z_mm_minmax": (z_min * self.pix_size_mm, z_max * self.pix_size_mm),
184
- }
185
- return DictToObj(res)
186
-
187
- def get_informative_string(self):
188
- doable_span_v = self.get_doable_span()
189
- if self.z_pix_per_proj[-1] >= self.z_pix_per_proj[-1]:
190
- direction = "ascending"
191
- else:
192
- direction = "descending"
193
-
194
- s = f"""
195
- Doable vertical span
196
- --------------------
197
- The scan has been performed with an {direction} vertical translation of the rotation axis.
198
-
199
- The detector vertical axis is up side down.
200
-
201
- Detector reference system at iproj=0:
202
- from vertical view height ... {doable_span_v.view_heights_minmax[0]}
203
- up to (included) ... {doable_span_v.view_heights_minmax[1]}
204
-
205
- The slice that projects to the first line of the first projection
206
- corresponds to vertical heigth = 0
207
-
208
- In voxels, the vertical doable span measures: {doable_span_v.z_pix_minmax[1] - doable_span_v.z_pix_minmax[0]}
209
-
210
- And in millimiters above the stage:
211
- from vertical height above stage ( mm units) ... {doable_span_v.z_mm_minmax[0] - self.z_offset_mm }
212
- up to (included) ... {doable_span_v.z_mm_minmax[1] - self.z_offset_mm }
213
- """
214
- return s
215
-
216
- def get_chunk_info(self, span_v_absolute):
217
- """
218
-
219
- This method returns an object containing all the informations that are needed to reconstruct
220
- the corresponding chunk
221
-
222
- angle_index_span: a pair of integers indicating the start and the end of useful angles
223
- in the array of all the scan angle self.projection_angles_deg
224
- span_v: a pair of two integers indicating the start and end of the span relatively to the lowest value
225
- of array self.total_view_heights
226
- integer_shift_v: an array, containing for each one of the useful projections of the span,
227
- the integer part of vertical shift to be used in cropping,
228
- fract_complement_to_integer_shift_v :
229
- the fractional remainder for cropping.
230
- z_pix_per_proj: an array, containing for each to be used projection of the span
231
- the vertical shift
232
- x_pix_per_proj: ....the horizontal shit
233
- angles_rad : an array, for each useful projection of the chunk the angle in radian
234
-
235
- Parameters:
236
- -----------
237
- span_v_absolute: tuple of integers
238
- a pair of two integers
239
- the first view height ( referred to the detector y axis at iproj=0)
240
- the second view height
241
- with the first height smaller than the second.
242
- """
243
- span_v = (span_v_absolute[0] - self.total_view_heights[0], span_v_absolute[1] - self.total_view_heights[0])
244
-
245
- sunshine_subset = self.sunshine_image[span_v[0] : span_v[1]]
246
- angular_profile = sunshine_subset.sum(axis=0)
247
-
248
- angle_indexes = np.arange(len(self.projection_angles_deg_internally))[angular_profile > 0]
249
-
250
- angle_index_span = angle_indexes.min(), angle_indexes.max() + 1
251
- if not (np.less(0, angular_profile[angle_index_span[0] : angle_index_span[1]]).all()):
252
- message = """ Something wrong occurred in the span preprocessing.
253
- It appears that some intermediate slices are not doables.
254
- The doable span should instead be contiguous. Please signal the problem"""
255
- raise RuntimeError(message)
256
-
257
- chunk_angles_deg = self.projection_angles_deg[angle_indexes]
258
-
259
- my_slicer = slice(angle_index_span[0], angle_index_span[1])
260
- values = (
261
- angle_index_span,
262
- span_v_absolute,
263
- self.integer_shift_v[my_slicer],
264
- self.fract_complement_to_integer_shift_v[my_slicer],
265
- self.z_pix_per_proj[my_slicer],
266
- self.x_pix_per_proj[my_slicer],
267
- np.deg2rad(chunk_angles_deg) * (1 - 2 * int(self.angles_are_inverted)),
268
- )
269
-
270
- key_names = (
271
- "angle_index_span",
272
- "span_v",
273
- "integer_shift_v",
274
- "fract_complement_to_integer_shift_v",
275
- "z_pix_per_proj",
276
- "x_pix_per_proj",
277
- "angles_rad",
278
- )
279
-
280
- return DictToObj(dict(zip(key_names, values)))
281
-
282
- def _setup_ephemerides(self):
283
- """
284
- A function which will set :
285
-
286
- * self.integer_shift_v
287
- * self.fract_complement_to_integer_shift_v
288
- * self.total_view_heights
289
- * self.on_detector_projection_intervals
290
- * self.within_margin_projection_intervals
291
- """
292
-
293
- for i_pro in range(self.total_num_images):
294
- trans_v = self.z_pix_per_proj[i_pro]
295
- self.integer_shift_v[i_pro] = math.ceil(trans_v)
296
- self.fract_complement_to_integer_shift_v[i_pro] = math.ceil(trans_v) - trans_v
297
-
298
- ## The two following line initialize the view height, then considering the vertical translation
299
- # the filed of view will be expanded
300
- total_view_top = self.detector_shape_vh[0]
301
- total_view_bottom = 0
302
-
303
- total_view_top = max(total_view_top, int(math.ceil(total_view_top + self.z_pix_per_proj.max())))
304
- total_view_bottom = min(total_view_bottom, int(math.floor(total_view_bottom + self.z_pix_per_proj.min())))
305
-
306
- self.total_view_heights = np.arange(total_view_bottom, total_view_top + 1)
307
-
308
- ## where possible only data from within safe phase margin will be considered. (within_margin)
309
- ## if it is enough for 360 or more degree.
310
- ## If it is not enough we'll complete wih data close to the border, provided that data comes from within detector
311
- ## This will be
312
- ## the case for the first and last doable slices.
313
- self.within_margin_projection_intervals = np.zeros(self.total_view_heights.shape + (2,), "i")
314
- self.on_detector_projection_intervals = np.zeros(self.total_view_heights.shape + (2,), "i")
315
-
316
- self.on_detector_projection_intervals[:, 1] = 0 # empty intervals
317
- self.within_margin_projection_intervals[:, 1] = 0
318
-
319
- for i_h, height in enumerate(self.total_view_heights):
320
- previous_is_inside_detector = False
321
- previous_is_inside_margin = False
322
-
323
- pos_inside_filtered_v = height - self.integer_shift_v
324
-
325
- is_inside_detector = np.less_equal(0, pos_inside_filtered_v)
326
- is_inside_detector *= np.less(
327
- pos_inside_filtered_v, self.detector_shape_vh[0] - np.less(0, self.fract_complement_to_integer_shift_v)
328
- )
329
-
330
- is_inside_margin = np.less_equal(self.phase_margin_pix, pos_inside_filtered_v)
331
- is_inside_margin *= np.less(
332
- pos_inside_filtered_v,
333
- self.detector_shape_vh[0]
334
- - self.phase_margin_pix
335
- - np.less(0, self.fract_complement_to_integer_shift_v),
336
- )
337
-
338
- tmp = np.arange(self.total_num_images)[is_inside_detector]
339
- if len(tmp):
340
- self.on_detector_projection_intervals[i_h, :] = (tmp.min(), tmp.max())
341
-
342
- tmp = np.arange(self.total_num_images)[is_inside_detector]
343
- if len(tmp):
344
- self.within_margin_projection_intervals[i_h, :] = (tmp.min(), tmp.max())
345
-
346
- def _setup_sunshine(self):
347
- """It prepares
348
-
349
- * self.sunshine_image
350
-
351
- an image which for every height, contained in self.total_view_heights, and in the same order,
352
- contains the list of factors, one per every projection of the total list. Each factor is a backprojection
353
- weight. A non-doable height corresponds to a line full of zeros.
354
- A doable height must correspond to a line having one and only one segment of contiguous non zero elements.
355
- """
356
-
357
- self.sunshine_image = np.zeros(self.total_view_heights.shape + (self.total_num_images,), "f")
358
-
359
- avg_angular_step_deg = np.diff(self.projection_angles_deg_internally).mean()
360
-
361
- projection_angles_for_interp = np.concatenate(
362
- [
363
- [self.projection_angles_deg_internally[0] - avg_angular_step_deg],
364
- self.projection_angles_deg_internally,
365
- [self.projection_angles_deg_internally[-1] + avg_angular_step_deg],
366
- ]
367
- )
368
-
369
- data_container_for_interp = np.zeros_like(projection_angles_for_interp)
370
-
371
- num_angular_periods = math.ceil(
372
- (self.projection_angles_deg_internally.max() - self.projection_angles_deg_internally.min()) / 360
373
- )
374
-
375
- for i_h, height in enumerate(self.total_view_heights):
376
- first_last_on_dect = self.on_detector_projection_intervals[i_h]
377
- first_last_within_margin = self.within_margin_projection_intervals[i_h]
378
-
379
- if first_last_on_dect[1] == 0:
380
- # this line never entered in the fov
381
- continue
382
-
383
- angle_on_dect_first_last = self.projection_angles_deg_internally[first_last_on_dect]
384
- angle_within_margin_first_last = self.projection_angles_deg_internally[first_last_within_margin]
385
-
386
- # a mask which is positive for angular positions for which the height i_h gets projected within the detector
387
- mask_on_dect = (
388
- np.less_equal(angle_on_dect_first_last[0], self.projection_angles_deg_internally)
389
- * np.less_equal(self.projection_angles_deg_internally, angle_on_dect_first_last[1])
390
- ).astype("f")
391
-
392
- # a mask which is positive for angular positions for which the height i_h gets projected within the margins
393
- mask_within_margin = (
394
- np.less_equal(angle_within_margin_first_last[0], self.projection_angles_deg_internally)
395
- * np.less_equal(self.projection_angles_deg_internally, angle_within_margin_first_last[1])
396
- ).astype("f")
397
-
398
- ## create a line which collects contributions from redundant angles
399
- detector_collector = np.zeros(self.projection_angles_deg_internally.shape, "f")
400
- margin_collector = np.zeros(self.projection_angles_deg_internally.shape, "f")
401
-
402
- # the following loop tracks, for each projection, the total weight available at the projection angle
403
- # The additional weight is coming from redundant angles.
404
- # In this sense the sunshine_image implements a first rudimentary reweighting,
405
- # which could be in principle used in the full pipeline, althought the regridded pipeline
406
- # implements a, better, reweighting o its own.
407
- for i_shift in range(-num_angular_periods, num_angular_periods + 1):
408
- signus = (
409
- 1 if (self.projection_angles_deg_internally[-1] > self.projection_angles_deg_internally[0]) else -1
410
- )
411
-
412
- data_container_for_interp[1:-1] = mask_on_dect
413
-
414
- detector_collector = detector_collector + mask_on_dect * np.interp(
415
- (self.projection_angles_deg_internally + i_shift * 360) * signus,
416
- signus * projection_angles_for_interp,
417
- data_container_for_interp,
418
- left=0,
419
- right=0,
420
- )
421
-
422
- data_container_for_interp[1:-1] = mask_within_margin
423
-
424
- margin_collector = margin_collector + mask_within_margin * np.interp(
425
- (self.projection_angles_deg_internally + i_shift * 360) * signus,
426
- signus * projection_angles_for_interp,
427
- data_container_for_interp,
428
- left=0,
429
- right=0,
430
- )
431
-
432
- detector_shined_angles = self.projection_angles_deg_internally[detector_collector > 0.99]
433
- margin_shined_angles = self.projection_angles_deg_internally[margin_collector > 0.99]
434
-
435
- if not len(detector_shined_angles) > 1:
436
- continue
437
-
438
- avg_step_deg = abs(avg_angular_step_deg)
439
-
440
- if len(margin_shined_angles):
441
- angular_span_safe_margin = (
442
- margin_shined_angles.max()
443
- - margin_shined_angles.min()
444
- + avg_step_deg * (1.01 + self.angular_tolerance_steps)
445
- )
446
- else:
447
- angular_span_safe_margin = 0
448
-
449
- angular_span_bare_border = (
450
- detector_shined_angles.max()
451
- - detector_shined_angles.min()
452
- + avg_step_deg * (1.01 + self.angular_tolerance_steps)
453
- )
454
-
455
- if not self.require_redundancy:
456
- if angular_span_safe_margin >= 360:
457
- self.sunshine_image[i_h] = margin_collector
458
- elif angular_span_bare_border >= 360:
459
- self.sunshine_image[i_h] = detector_collector
460
- else:
461
- redundancy_angle_deg = 360
462
- if angular_span_safe_margin >= 360 and angular_span_safe_margin > 2 * (
463
- redundancy_angle_deg + avg_step_deg
464
- ):
465
- self.sunshine_image[i_h] = margin_collector
466
- elif angular_span_bare_border >= 360 and angular_span_bare_border > 2 * (
467
- redundancy_angle_deg + avg_step_deg
468
- ):
469
- self.sunshine_image[i_h] = detector_collector
470
-
471
- sunshine_mask = np.less(0.99, self.sunshine_image)
472
-
473
- self.sunshine_image[np.array([True]) ^ sunshine_mask] = 1.0
474
- self.sunshine_image[:] = 1 / self.sunshine_image
475
- self.sunshine_image[np.array([True]) ^ sunshine_mask] = 0.0
476
-
477
- shp = self.sunshine_image.shape
478
- X, Y = np.meshgrid(np.arange(shp[1]), np.arange(shp[0]))
479
-
480
- condition = self.sunshine_image > 0
481
- self.sunshine_starts = X.min(axis=1, initial=shp[1], where=condition)
482
- self.sunshine_ends = X.max(axis=1, initial=0, where=condition)
483
- self.sunshine_ends[self.sunshine_ends > 0] += 1
@@ -1,157 +0,0 @@
1
- from nabu.pipeline.helical import gridded_accumulator, span_strategy
2
- from nabu.testutils import get_data
3
-
4
- import pytest
5
- import numpy as np
6
- import os
7
- import h5py
8
-
9
-
10
- @pytest.fixture(scope="class")
11
- def bootstrap(request):
12
- cls = request.cls
13
-
14
- # This is a helical dataset derived
15
- # from "crayon" dataset, using 5 slices and covering 2.5 x 360 angular span
16
- # in halftomo, with vertical translations.
17
-
18
- helical_dataset = get_data("small_sparse_helical_dataset.npz")
19
-
20
- helical_dataset = dict([item for item in helical_dataset.items()])
21
- # the radios, in the dataset file, are stored by swapping angular and x dimension
22
- # so that the fast running dimension runs over the projections.
23
- # Due to the sparsity of the dataset, where only an handful of slices
24
- # has signal, this gives a much better compression even when the axis is translating
25
- # vertically
26
- helical_dataset["radios"] = np.array(np.swapaxes(helical_dataset["radios_transposed"], 0, 2))
27
- del helical_dataset["radios_transposed"]
28
-
29
- # adding members: radios, dark, flats, z_pix_per_proj, x_pix_per_proj, projection_angles_deg, pixel_size_mm, phase_margin_pix,
30
- # weigth_field=weigth_field, double_flat
31
- dataset_keys = [
32
- "dark",
33
- "flats",
34
- "z_pix_per_proj",
35
- "x_pix_per_proj",
36
- "projection_angles_deg",
37
- "pixel_size_mm",
38
- "phase_margin_pix",
39
- "weights_field",
40
- "double_flat",
41
- "rotation_axis_position",
42
- "detector_shape_vh",
43
- "result_inset",
44
- "radios",
45
- ]
46
- for key in dataset_keys:
47
- setattr(cls, key, helical_dataset[key])
48
-
49
- cls.rtol_regridded = 1.0e-6
50
-
51
-
52
- @pytest.mark.usefixtures("bootstrap")
53
- class TestGriddedAccumulator:
54
- """
55
- Test the GriddedAccumulator.
56
- Rebuilds the sinogram for some selected slices of the crayon dataset
57
- """
58
-
59
- def test_regridding(self):
60
- span_info = span_strategy.SpanStrategy(
61
- z_pix_per_proj=self.z_pix_per_proj,
62
- x_pix_per_proj=self.x_pix_per_proj,
63
- detector_shape_vh=self.detector_shape_vh,
64
- phase_margin_pix=self.phase_margin_pix,
65
- projection_angles_deg=self.projection_angles_deg,
66
- require_redundancy=True,
67
- pixel_size_mm=self.pixel_size_mm,
68
- logger=None,
69
- )
70
-
71
- # I would like to reconstruct from feaseable height 15 to feaseable height 18
72
- # relatively to the first doable slice in the vertical translation direction
73
- # I get the heights in the detector frame of the first and of the last
74
-
75
- reconstruction_space = gridded_accumulator.get_reconstruction_space(
76
- span_info=span_info, min_scanwise_z=15, end_scanwise_z=18, phase_margin_pix=self.phase_margin_pix
77
- )
78
-
79
- chunk_info = span_info.get_chunk_info((reconstruction_space.my_z_min, reconstruction_space.my_z_end))
80
-
81
- sub_region = (
82
- reconstruction_space.my_z_min - self.phase_margin_pix,
83
- reconstruction_space.my_z_end + self.phase_margin_pix,
84
- )
85
-
86
- ## useful projections
87
- proj_num_start, proj_num_end = chunk_info.angle_index_span
88
-
89
- # the first of the chunk angular range
90
- my_first_pnum = proj_num_start
91
-
92
- self.accumulator = gridded_accumulator.GriddedAccumulator(
93
- gridded_radios=reconstruction_space.gridded_radios,
94
- gridded_weights=reconstruction_space.gridded_cumulated_weights,
95
- diagnostic_radios=reconstruction_space.diagnostic_radios,
96
- diagnostic_weights=reconstruction_space.diagnostic_weights,
97
- diagnostic_angles=reconstruction_space.diagnostic_proj_angle,
98
- diagnostic_searched_angles_rad_clipped=reconstruction_space.diagnostic_searched_angles_rad_clipped,
99
- diagnostic_zpix_transl=reconstruction_space.diagnostic_zpix_transl,
100
- dark=self.dark,
101
- flat_indexes=[0, 7501],
102
- flats=self.flats,
103
- weights=self.weights_field,
104
- double_flat=self.double_flat,
105
- diag_zpro_run=0,
106
- )
107
-
108
- # splitting in sub ranges of 100 projections
109
- n_granularity = 100
110
- pnum_start_list = list(np.arange(proj_num_start, proj_num_end, n_granularity))
111
- pnum_end_list = pnum_start_list[1:] + [proj_num_end]
112
-
113
- for pnum_start, pnum_end in zip(pnum_start_list, pnum_end_list):
114
- start_in_chunk = pnum_start - my_first_pnum
115
- end_in_chunk = pnum_end - my_first_pnum
116
-
117
- self._read_data_and_apply_flats(
118
- slice(pnum_start, pnum_end), slice(start_in_chunk, end_in_chunk), chunk_info, sub_region, span_info
119
- )
120
-
121
- res = reconstruction_space.gridded_radios / reconstruction_space.gridded_cumulated_weights
122
-
123
- # check only a sub part to avoid further increasing of the file on edna site
124
- errmax = np.max(np.abs(res[:200, 1, -500:] - self.result_inset) / np.max(res))
125
- assert errmax < self.rtol_regridded, "Max error is too high"
126
-
127
- # uncomment this to see
128
- # h5py.File("processed_sinogram.h5","w")["sinogram"] = res
129
-
130
- def _read_data_and_apply_flats(self, sub_total_prange_slice, subchunk_slice, chunk_info, sub_region, span_info):
131
- my_integer_shifts_v = chunk_info.integer_shift_v[subchunk_slice]
132
- fract_complement_shifts_v = chunk_info.fract_complement_to_integer_shift_v[subchunk_slice]
133
- x_shifts_list = chunk_info.x_pix_per_proj[subchunk_slice]
134
- subr_start_z, subr_end_z = sub_region
135
-
136
- subr_start_z_list = subr_start_z - my_integer_shifts_v
137
- subr_end_z_list = subr_end_z - my_integer_shifts_v + 1
138
-
139
- dtasrc_start_z = max(0, subr_start_z_list.min())
140
- dtasrc_end_z = min(span_info.detector_shape_vh[0], subr_end_z_list.max())
141
-
142
- data_raw = self.radios[sub_total_prange_slice, slice(dtasrc_start_z, dtasrc_end_z), :]
143
-
144
- subsampling_file_slice = sub_total_prange_slice
145
-
146
- # my_subsampled_indexes = self.chunk_reader._sorted_files_indices[subsampling_file_slice]
147
- my_subsampled_indexes = (np.arange(10000))[subsampling_file_slice]
148
-
149
- self.accumulator.extract_preprocess_with_flats(
150
- subchunk_slice,
151
- my_subsampled_indexes,
152
- chunk_info,
153
- np.array((subr_start_z, subr_end_z), "i"),
154
- np.array((dtasrc_start_z, dtasrc_end_z), "i"),
155
- data_raw,
156
- sub_total_prange_slice,
157
- )