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
@@ -1,563 +0,0 @@
1
- from distutils.version import StrictVersion
2
- from typing import Optional, Union
3
- import logging
4
- import functools
5
- import numpy
6
- from scipy.ndimage import affine_transform
7
- from tomoscan.scanbase import TomoScanBase
8
- from tomoscan.volumebase import VolumeBase
9
- from nxtomo.utils.transformation import build_matrix, UDDetTransformation
10
- from silx.utils.enum import Enum as _Enum
11
- from scipy.fft import rfftn as local_fftn
12
- from scipy.fft import irfftn as local_ifftn
13
- from silx.utils.enum import Enum as _Enum
14
- from nxtomo.utils.transformation import build_matrix, UDDetTransformation
15
- from tomoscan.scanbase import TomoScanBase
16
- from .overlap import OverlapStitchingStrategy, ZStichOverlapKernel
17
- from .alignment import AlignmentAxis1, AlignmentAxis2, PaddedRawData
18
- from ..misc import fourier_filters
19
- from ..estimation.alignment import AlignmentBase
20
- from ..resources.dataset_analyzer import HDF5DatasetAnalyzer
21
- from ..resources.nxflatfield import update_dataset_info_flats_darks
22
-
23
- try:
24
- import itk
25
- except ImportError:
26
- has_itk = False
27
- else:
28
- has_itk = True
29
-
30
- _logger = logging.getLogger(__name__)
31
-
32
-
33
- try:
34
- from skimage.registration import phase_cross_correlation
35
- except ImportError:
36
- _logger.warning(
37
- "Unable to load skimage. Please install it if you want to use it for finding shifts from `find_relative_shifts`"
38
- )
39
- __has_sk_phase_correlation__ = False
40
- else:
41
- __has_sk_phase_correlation__ = True
42
-
43
-
44
- class ShiftAlgorithm(_Enum):
45
- """All generic shift search algorithm"""
46
-
47
- NABU_FFT = "nabu-fft"
48
- SKIMAGE = "skimage"
49
- ITK_IMG_REG_V4 = "itk-img-reg-v4"
50
- NONE = "None"
51
-
52
- # In the case of shift search on radio along axis 2 (or axis x in image space) we can benefit from the existing
53
- # nabu algorithm such as growing-window or sliding-window
54
- CENTERED = "centered"
55
- GLOBAL = "global"
56
- SLIDING_WINDOW = "sliding-window"
57
- GROWING_WINDOW = "growing-window"
58
- SINO_COARSE_TO_FINE = "sino-coarse-to-fine"
59
- COMPOSITE_COARSE_TO_FINE = "composite-coarse-to-fine"
60
-
61
- @classmethod
62
- def from_value(cls, value):
63
- if value in ("", None):
64
- return ShiftAlgorithm.NONE
65
- else:
66
- return super().from_value(value=value)
67
-
68
-
69
- def test_overlap_stitching_strategy(overlap_1, overlap_2, stitching_strategies):
70
- """
71
- stitch the two ovrelap with all the requested strategies.
72
- Return a dictionary with stitching strategy as key and a result dict as value.
73
- result dict keys are: 'weights_overlap_1', 'weights_overlap_2', 'stiching'
74
- """
75
- res = {}
76
- for strategy in stitching_strategies:
77
- s = OverlapStitchingStrategy.from_value(strategy)
78
- stitcher = ZStichOverlapKernel(
79
- stitching_strategy=s,
80
- frame_width=overlap_1.shape[1],
81
- )
82
- stiched_overlap, w1, w2 = stitcher.stitch(overlap_1, overlap_2, check_input=True)
83
- res[s.value] = {
84
- "stitching": stiched_overlap,
85
- "weights_overlap_1": w1,
86
- "weights_overlap_2": w2,
87
- }
88
- return res
89
-
90
-
91
- def find_frame_relative_shifts(
92
- overlap_upper_frame: numpy.ndarray,
93
- overlap_lower_frame: numpy.ndarray,
94
- estimated_shifts,
95
- x_cross_correlation_function=None,
96
- y_cross_correlation_function=None,
97
- x_shifts_params: Optional[dict] = None,
98
- y_shifts_params: Optional[dict] = None,
99
- ):
100
- from nabu.stitching.config import (
101
- KEY_WINDOW_SIZE,
102
- KEY_LOW_PASS_FILTER,
103
- KEY_HIGH_PASS_FILTER,
104
- ) # avoid cyclic import
105
-
106
- x_cross_correlation_function = ShiftAlgorithm.from_value(x_cross_correlation_function)
107
- y_cross_correlation_function = ShiftAlgorithm.from_value(y_cross_correlation_function)
108
-
109
- if x_shifts_params is None:
110
- x_shifts_params = {}
111
-
112
- if y_shifts_params is None:
113
- y_shifts_params = {}
114
-
115
- # apply filtering if any
116
- def _str_to_int(value):
117
- if isinstance(value, str):
118
- value = value.lstrip("'").lstrip('"')
119
- value = value.rstrip("'").rstrip('"')
120
- value = int(value)
121
- return value
122
-
123
- low_pass = _str_to_int(x_shifts_params.get(KEY_LOW_PASS_FILTER, y_shifts_params.get(KEY_LOW_PASS_FILTER, None)))
124
- high_pass = _str_to_int(x_shifts_params.get(KEY_HIGH_PASS_FILTER, y_shifts_params.get(KEY_HIGH_PASS_FILTER, None)))
125
- if high_pass is None and low_pass is None:
126
- pass
127
- else:
128
- if low_pass is None:
129
- low_pass = 1
130
- if high_pass is None:
131
- high_pass = 20
132
- _logger.info(f"filter image for shift search (low_pass={low_pass}, high_pass={high_pass})")
133
- img_filter = fourier_filters.get_bandpass_filter(
134
- overlap_upper_frame.shape[-2:],
135
- cutoff_lowpass=low_pass,
136
- cutoff_highpass=high_pass,
137
- use_rfft=True,
138
- data_type=overlap_upper_frame.dtype,
139
- )
140
- overlap_upper_frame = local_ifftn(
141
- local_fftn(overlap_upper_frame, axes=(-2, -1)) * img_filter, axes=(-2, -1)
142
- ).real
143
- overlap_lower_frame = local_ifftn(
144
- local_fftn(overlap_lower_frame, axes=(-2, -1)) * img_filter, axes=(-2, -1)
145
- ).real
146
-
147
- # compute shifts
148
- initial_shifts = numpy.array(estimated_shifts).copy()
149
- extra_shifts = numpy.array([0.0, 0.0])
150
-
151
- def skimage_proxy(img1, img2):
152
- if not __has_sk_phase_correlation__:
153
- raise ValueError("scikit-image not installed. Cannot do phase correlation from it")
154
- else:
155
- found_shift, _, _ = phase_cross_correlation(reference_image=img1, moving_image=img2, space="real")
156
- return -found_shift
157
-
158
- shift_methods = {
159
- ShiftAlgorithm.NABU_FFT: functools.partial(
160
- find_shift_correlate, img1=overlap_upper_frame, img2=overlap_lower_frame
161
- ),
162
- ShiftAlgorithm.SKIMAGE: functools.partial(skimage_proxy, img1=overlap_upper_frame, img2=overlap_lower_frame),
163
- ShiftAlgorithm.ITK_IMG_REG_V4: functools.partial(
164
- find_shift_with_itk, img1=overlap_upper_frame, img2=overlap_lower_frame
165
- ),
166
- ShiftAlgorithm.NONE: functools.partial(lambda: (0.0, 0.0)),
167
- }
168
-
169
- res_algo = {}
170
- for shift_alg in set((x_cross_correlation_function, y_cross_correlation_function)):
171
- if shift_alg not in shift_methods:
172
- raise ValueError(f"requested image alignment function not handled ({shift_alg})")
173
- try:
174
- res_algo[shift_alg] = shift_methods[shift_alg]()
175
- except Exception as e:
176
- _logger.error(f"Failed to find shift from {shift_alg.value}. Error is {e}")
177
- res_algo[shift_alg] = (0, 0)
178
-
179
- extra_shifts = (
180
- res_algo[y_cross_correlation_function][0],
181
- res_algo[x_cross_correlation_function][1],
182
- )
183
-
184
- final_rel_shifts = numpy.array(extra_shifts) + initial_shifts
185
- return tuple([int(shift) for shift in final_rel_shifts])
186
-
187
-
188
- def find_volumes_relative_shifts(
189
- upper_volume: VolumeBase,
190
- lower_volume: VolumeBase,
191
- estimated_shifts,
192
- dim_axis_1: int,
193
- dtype,
194
- flip_ud_upper_frame: bool = False,
195
- flip_ud_lower_frame: bool = False,
196
- slice_for_shift: Union[int, str] = "middle",
197
- x_cross_correlation_function=None,
198
- y_cross_correlation_function=None,
199
- x_shifts_params: Optional[dict] = None,
200
- y_shifts_params: Optional[dict] = None,
201
- alignment_axis_2="center",
202
- alignment_axis_1="center",
203
- ):
204
- """
205
-
206
- :param int dim_axis_1: axis 1 dimension (to handle axis 1 alignment)
207
- """
208
- if y_shifts_params is None:
209
- y_shifts_params = {}
210
-
211
- if x_shifts_params is None:
212
- x_shifts_params = {}
213
-
214
- alignment_axis_2 = AlignmentAxis2.from_value(alignment_axis_2)
215
- alignment_axis_1 = AlignmentAxis1.from_value(alignment_axis_1)
216
- assert dim_axis_1 > 0, "dim_axis_1 <= 0"
217
-
218
- if isinstance(slice_for_shift, str):
219
- if slice_for_shift == "first":
220
- slice_for_shift = 0
221
- elif slice_for_shift == "last":
222
- slice_for_shift = dim_axis_1
223
- elif slice_for_shift == "middle":
224
- slice_for_shift = dim_axis_1 // 2
225
- else:
226
- raise ValueError("invalid slice provided to search shift", slice_for_shift)
227
-
228
- def get_slice_along_axis_1(volume: VolumeBase, index: int):
229
- assert isinstance(index, int), f"index should be an int, {type(index)} provided"
230
- volume_shape = volume.get_volume_shape()
231
- if alignment_axis_1 is AlignmentAxis1.BACK:
232
- front_empty_width = dim_axis_1 - volume_shape[1]
233
- if index < front_empty_width:
234
- return PaddedRawData.get_empty_frame(shape=(volume_shape[0], volume_shape[2]), dtype=dtype)
235
- else:
236
- return volume.get_slice(index=index - front_empty_width, axis=1)
237
- elif alignment_axis_1 is AlignmentAxis1.FRONT:
238
- if index >= volume_shape[1]:
239
- return PaddedRawData.get_empty_frame(shape=(volume_shape[0], volume_shape[2]), dtype=dtype)
240
- else:
241
- return volume.get_slice(index=index, axis=1)
242
- elif alignment_axis_1 is AlignmentAxis1.CENTER:
243
- front_empty_width = (dim_axis_1 - volume_shape[1]) // 2
244
- back_empty_width = dim_axis_1 - front_empty_width
245
- if index < front_empty_width or index > back_empty_width:
246
- return PaddedRawData.get_empty_frame(shape=(volume_shape[0], volume_shape[2]), dtype=dtype)
247
- else:
248
- return volume.get_slice(index=index - front_empty_width, axis=1)
249
- else:
250
- raise TypeError(f"unmanaged alignment mode {alignment_axis_1.value}")
251
-
252
- upper_frame = get_slice_along_axis_1(upper_volume, index=slice_for_shift)
253
- lower_frame = get_slice_along_axis_1(lower_volume, index=slice_for_shift)
254
- if flip_ud_upper_frame:
255
- upper_frame = numpy.flipud(upper_frame.copy())
256
- if flip_ud_lower_frame:
257
- lower_frame = numpy.flipud(lower_frame.copy())
258
-
259
- from nabu.stitching.config import KEY_WINDOW_SIZE # avoid cyclic import
260
-
261
- w_window_size = int(y_shifts_params.get(KEY_WINDOW_SIZE, 400))
262
- start_overlap = max(estimated_shifts[0] // 2 - w_window_size // 2, 0)
263
- end_overlap = min(estimated_shifts[0] // 2 + w_window_size // 2, min(upper_frame.shape[0], lower_frame.shape[0]))
264
-
265
- if start_overlap == 0:
266
- overlap_upper_frame = upper_frame[-end_overlap:]
267
- else:
268
- overlap_upper_frame = upper_frame[-end_overlap:-start_overlap]
269
- overlap_lower_frame = lower_frame[start_overlap:end_overlap]
270
-
271
- # align if necessary
272
- if overlap_upper_frame.shape[1] != overlap_lower_frame.shape[1]:
273
- overlap_frame_width = min(overlap_upper_frame.shape[1], overlap_lower_frame.shape[1])
274
- if alignment_axis_2 is AlignmentAxis2.CENTER:
275
- upper_frame_left_pos = overlap_upper_frame.shape[1] // 2 - overlap_frame_width // 2
276
- upper_frame_right_pos = upper_frame_left_pos + overlap_frame_width
277
- overlap_upper_frame = overlap_upper_frame[:, upper_frame_left_pos:upper_frame_right_pos]
278
-
279
- lower_frame_left_pos = overlap_lower_frame.shape[1] // 2 - overlap_frame_width // 2
280
- lower_frame_right_pos = lower_frame_left_pos + overlap_frame_width
281
- overlap_lower_frame = overlap_lower_frame[:, lower_frame_left_pos:lower_frame_right_pos]
282
- elif alignment_axis_2 is AlignmentAxis2.LEFT:
283
- overlap_upper_frame = overlap_upper_frame[:, :overlap_frame_width]
284
- overlap_lower_frame = overlap_lower_frame[:, :overlap_frame_width]
285
- elif alignment_axis_2 is AlignmentAxis2.RIGTH:
286
- overlap_upper_frame = overlap_upper_frame[:, -overlap_frame_width:]
287
- overlap_lower_frame = overlap_lower_frame[:, -overlap_frame_width:]
288
- else:
289
- raise ValueError(f"Alignement {alignment_axis_2.value} is not handled")
290
-
291
- if not overlap_upper_frame.shape == overlap_lower_frame.shape:
292
- raise ValueError(f"Fail to get consistant overlap ({overlap_upper_frame.shape} vs {overlap_lower_frame.shape})")
293
-
294
- return find_frame_relative_shifts(
295
- overlap_upper_frame=overlap_upper_frame,
296
- overlap_lower_frame=overlap_lower_frame,
297
- estimated_shifts=estimated_shifts,
298
- x_cross_correlation_function=x_cross_correlation_function,
299
- y_cross_correlation_function=y_cross_correlation_function,
300
- x_shifts_params=x_shifts_params,
301
- y_shifts_params=y_shifts_params,
302
- )
303
-
304
-
305
- from nabu.pipeline.estimators import estimate_cor
306
-
307
-
308
- def find_projections_relative_shifts(
309
- upper_scan: TomoScanBase,
310
- lower_scan: TomoScanBase,
311
- estimated_shifts,
312
- flip_ud_upper_frame: bool = False,
313
- flip_ud_lower_frame: bool = False,
314
- projection_for_shift: Union[int, str] = "middle",
315
- invert_order: bool = False,
316
- x_cross_correlation_function=None,
317
- y_cross_correlation_function=None,
318
- x_shifts_params: Optional[dict] = None,
319
- y_shifts_params: Optional[dict] = None,
320
- ) -> tuple:
321
- """
322
- deduce the relative shift between the two scans.
323
- Expected behavior:
324
- * compute expected overlap area from z_translations and (sample) pixel size
325
- * call an (optional) cross correlation function from the overlap area to compute the x shift and polish the y shift from `projection_for_shift`
326
-
327
- :param TomoScanBase scan_0:
328
- :param TomoScanBase scan_1:
329
- :param int axis_0_overlap_px: overlap between the two scans in pixel
330
- :param Union[int,str] projection_for_shift: index fo the projection to use (in projection space or in scan space ?. For now in projection) or str. If str must be in (`middle`, `first`, `last`)
331
- :param str x_cross_correlation_function: optional method to refine x shift from computing cross correlation. For now valid values are: ("skimage", "nabu-fft")
332
- :param str y_cross_correlation_function: optional method to refine y shift from computing cross correlation. For now valid values are: ("skimage", "nabu-fft")
333
- :param int minimal_overlap_area_for_cross_correlation: if first approximated overlap shift found from z_translation is lower than this value will fall back on taking the full image for the cross correlation and log a warning
334
- :param bool invert_order: are projections inverted between the two scans (case if rotation angle are inverted)
335
- :param tuple estimated_shifts: 'a priori' shift estimation
336
- :return: relative shift of scan_1 with scan_0 as reference: (y_shift, x_shift)
337
- :rtype: tuple
338
-
339
- :warning: this function will flip left-right and up-down frames by default. So it will return shift according to this information
340
- """
341
- if x_shifts_params is None:
342
- x_shifts_params = {}
343
- if y_shifts_params is None:
344
- y_shifts_params = {}
345
- if estimated_shifts[0] < 0:
346
- raise ValueError("y_overlap_px is expected to be stricktly positive")
347
-
348
- x_cross_correlation_function = ShiftAlgorithm.from_value(x_cross_correlation_function)
349
- y_cross_correlation_function = ShiftAlgorithm.from_value(y_cross_correlation_function)
350
-
351
- # { handle specific use case (finding shift on scan) - when using nabu COR algorithms (for axis 2)
352
- if x_cross_correlation_function in (
353
- ShiftAlgorithm.SINO_COARSE_TO_FINE,
354
- ShiftAlgorithm.COMPOSITE_COARSE_TO_FINE,
355
- ShiftAlgorithm.CENTERED,
356
- ShiftAlgorithm.GLOBAL,
357
- ShiftAlgorithm.GROWING_WINDOW,
358
- ShiftAlgorithm.SLIDING_WINDOW,
359
- ):
360
- cor_options = x_shifts_params.copy()
361
- cor_options.pop("img_reg_method", None)
362
- # remove all none numeric options because estimate_cor will call 'literal_eval' on them
363
-
364
- upper_scan_dataset_info = HDF5DatasetAnalyzer(
365
- location=upper_scan.master_file, extra_options={"hdf5_entry": upper_scan.entry}
366
- )
367
- update_dataset_info_flats_darks(upper_scan_dataset_info, flatfield_mode=1)
368
-
369
- upper_scan_pos = estimate_cor(
370
- method=x_cross_correlation_function.value,
371
- dataset_info=upper_scan_dataset_info,
372
- cor_options=cor_options,
373
- )
374
- lower_scan_dataset_info = HDF5DatasetAnalyzer(
375
- location=lower_scan.master_file, extra_options={"hdf5_entry": lower_scan.entry}
376
- )
377
- update_dataset_info_flats_darks(lower_scan_dataset_info, flatfield_mode=1)
378
- lower_scan_pos = estimate_cor(
379
- method=x_cross_correlation_function.value,
380
- dataset_info=lower_scan_dataset_info,
381
- cor_options=cor_options,
382
- )
383
-
384
- estimated_shifts = tuple(
385
- [
386
- estimated_shifts[0],
387
- (lower_scan_pos - upper_scan_pos),
388
- ]
389
- )
390
- x_cross_correlation_function = ShiftAlgorithm.NONE
391
-
392
- # } else we will compute shift from the flat projections
393
-
394
- def get_flat_fielded_proj(
395
- scan: TomoScanBase, proj_index: int, reverse: bool, transformation_matrix: Optional[numpy.ndarray]
396
- ):
397
- first_proj_idx = sorted(lower_scan.projections.keys(), reverse=reverse)[proj_index]
398
- ff = scan.flat_field_correction(
399
- (scan.projections[first_proj_idx],),
400
- (first_proj_idx,),
401
- )[0]
402
- assert ff.ndim == 2, f"expects a single 2D frame. Get something with {ff.ndim} dimensions"
403
- if transformation_matrix is not None:
404
- assert (
405
- transformation_matrix.ndim == 2
406
- ), f"expects a 2D transformation matrix. Get a {transformation_matrix.ndim} D"
407
- if numpy.isclose(transformation_matrix[2, 2], -1):
408
- transformation_matrix[2, :] = 0
409
- transformation_matrix[0, 2] = 0
410
- transformation_matrix[2, 2] = 1
411
- ff = numpy.flipud(ff)
412
- return ff
413
-
414
- if isinstance(projection_for_shift, str):
415
- if projection_for_shift.lower() == "first":
416
- projection_for_shift = 0
417
- elif projection_for_shift.lower() == "last":
418
- projection_for_shift = -1
419
- elif projection_for_shift.lower() == "middle":
420
- projection_for_shift = len(upper_scan.projections) // 2
421
- else:
422
- try:
423
- projection_for_shift = int(projection_for_shift)
424
- except ValueError:
425
- raise ValueError(
426
- f"{projection_for_shift} cannot be cast to an int and is not one of the possible ('first', 'last', 'middle')"
427
- )
428
- elif not isinstance(projection_for_shift, (int, numpy.number)):
429
- raise TypeError(
430
- f"projection_for_shift is expected to be an int. Not {type(projection_for_shift)} - {projection_for_shift}"
431
- )
432
-
433
- upper_scan_transformations = list(upper_scan.get_detector_transformations(tuple()))
434
- if flip_ud_upper_frame:
435
- upper_scan_transformations.append(UDDetTransformation())
436
- upper_scan_trans_matrix = build_matrix(upper_scan_transformations)
437
- lower_scan_transformations = list(lower_scan.get_detector_transformations(tuple()))
438
- if flip_ud_lower_frame:
439
- lower_scan_transformations.append(UDDetTransformation())
440
- lower_scan_trans_matrix = build_matrix(lower_scan_transformations)
441
- upper_proj = get_flat_fielded_proj(
442
- upper_scan,
443
- projection_for_shift,
444
- reverse=False,
445
- transformation_matrix=upper_scan_trans_matrix,
446
- )
447
- lower_proj = get_flat_fielded_proj(
448
- lower_scan,
449
- projection_for_shift,
450
- reverse=invert_order,
451
- transformation_matrix=lower_scan_trans_matrix,
452
- )
453
-
454
- from nabu.stitching.config import KEY_WINDOW_SIZE # avoid cyclic import
455
-
456
- w_window_size = int(y_shifts_params.get(KEY_WINDOW_SIZE, 400))
457
- start_overlap = max(estimated_shifts[0] // 2 - w_window_size // 2, 0)
458
- end_overlap = min(estimated_shifts[0] // 2 + w_window_size // 2, min(upper_proj.shape[0], lower_proj.shape[0]))
459
- if start_overlap == 0:
460
- overlap_upper_frame = upper_proj[-end_overlap:]
461
- else:
462
- overlap_upper_frame = upper_proj[-end_overlap:-start_overlap]
463
- overlap_lower_frame = lower_proj[start_overlap:end_overlap]
464
- if not overlap_upper_frame.shape == overlap_lower_frame.shape:
465
- raise ValueError(f"Fail to get consistant overlap ({overlap_upper_frame.shape} vs {overlap_lower_frame.shape})")
466
-
467
- return find_frame_relative_shifts(
468
- overlap_upper_frame=overlap_upper_frame,
469
- overlap_lower_frame=overlap_lower_frame,
470
- estimated_shifts=estimated_shifts,
471
- x_cross_correlation_function=x_cross_correlation_function,
472
- y_cross_correlation_function=y_cross_correlation_function,
473
- x_shifts_params=x_shifts_params,
474
- y_shifts_params=y_shifts_params,
475
- )
476
-
477
-
478
- def find_shift_correlate(img1, img2, padding_mode="reflect"):
479
- alignment = AlignmentBase()
480
- cc = alignment._compute_correlation_fft(
481
- img1,
482
- img2,
483
- padding_mode,
484
- )
485
-
486
- img_shape = img1.shape[-2:]
487
- cc_vs = numpy.fft.fftfreq(img_shape[-2], 1 / img_shape[-2])
488
- cc_hs = numpy.fft.fftfreq(img_shape[-1], 1 / img_shape[-1])
489
-
490
- (f_vals, fv, fh) = alignment.extract_peak_region_2d(cc, cc_vs=cc_vs, cc_hs=cc_hs)
491
- shifts_vh = alignment.refine_max_position_2d(f_vals, fv, fh)
492
- return -shifts_vh
493
-
494
-
495
- def find_shift_with_itk(img1: numpy.ndarray, img2: numpy.ndarray) -> tuple:
496
- # created from https://examples.itk.org/src/registration/common/perform2dtranslationregistrationwithmeansquares/documentation
497
- # return (y_shift, x_shift). For now shift are integers as only integer shift are handled.
498
- if not img1.dtype == img2.dtype:
499
- raise ValueError("the two images are expected to have the same type")
500
- if not img1.ndim == img2.ndim == 2:
501
- raise ValueError("the two images are expected to 2D numpy arrays")
502
-
503
- if not has_itk:
504
- _logger.warning("itk is not installed. Please install it to find shift with it")
505
- return (0, 0)
506
-
507
- if StrictVersion(itk.Version.GetITKVersion()) < StrictVersion("4.9.0"):
508
- _logger.error("ITK 4.9.0 is required to find shift with it.")
509
- return (0, 0)
510
-
511
- pixel_type = itk.ctype("float")
512
- img1 = numpy.ascontiguousarray(img1, dtype=numpy.float32)
513
- img2 = numpy.ascontiguousarray(img2, dtype=numpy.float32)
514
-
515
- dimension = 2
516
- image_type = itk.Image[pixel_type, dimension]
517
-
518
- fixed_image = itk.PyBuffer[image_type].GetImageFromArray(img1)
519
- moving_image = itk.PyBuffer[image_type].GetImageFromArray(img2)
520
-
521
- transform_type = itk.TranslationTransform[itk.D, dimension]
522
- initial_transform = transform_type.New()
523
-
524
- optimizer = itk.RegularStepGradientDescentOptimizerv4.New(
525
- LearningRate=4,
526
- MinimumStepLength=0.001,
527
- RelaxationFactor=0.5,
528
- NumberOfIterations=200,
529
- )
530
-
531
- metric = itk.MeanSquaresImageToImageMetricv4[image_type, image_type].New()
532
-
533
- registration = itk.ImageRegistrationMethodv4.New(
534
- FixedImage=fixed_image,
535
- MovingImage=moving_image,
536
- Metric=metric,
537
- Optimizer=optimizer,
538
- InitialTransform=initial_transform,
539
- )
540
-
541
- moving_initial_transform = transform_type.New()
542
- initial_parameters = moving_initial_transform.GetParameters()
543
- initial_parameters[0] = 0
544
- initial_parameters[1] = 0
545
- moving_initial_transform.SetParameters(initial_parameters)
546
- registration.SetMovingInitialTransform(moving_initial_transform)
547
-
548
- identity_transform = transform_type.New()
549
- identity_transform.SetIdentity()
550
- registration.SetFixedInitialTransform(identity_transform)
551
-
552
- registration.SetNumberOfLevels(1)
553
- registration.SetSmoothingSigmasPerLevel([0])
554
- registration.SetShrinkFactorsPerLevel([1])
555
-
556
- registration.Update()
557
-
558
- transform = registration.GetTransform()
559
- final_parameters = transform.GetParameters()
560
- translation_along_x = final_parameters.GetElement(0)
561
- translation_along_y = final_parameters.GetElement(1)
562
-
563
- return numpy.round(translation_along_y), numpy.round(translation_along_x)