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
@@ -1,51 +0,0 @@
1
- #!/usr/bin/env python
2
- # -*- coding: utf-8 -*-
3
-
4
- import sys
5
- import os
6
- import pytest
7
- from nabu.utils import get_folder_path
8
- from nabu import __nabu_modules__ as nabu_modules
9
-
10
-
11
- def get_modules_to_test(mods):
12
- sep = os.sep
13
- modules = []
14
- extra_args = []
15
- for mod in mods:
16
- if mod.startswith("-"):
17
- extra_args.append(mod)
18
- continue
19
- # Test a whole module
20
- if mod.lower() in nabu_modules:
21
- mod_abspath = os.path.join(get_folder_path(mod), "tests")
22
- # Test an individual file
23
- else:
24
- mod_path = mod.replace(".", sep) + ".py"
25
- mod_abspath = get_folder_path(mod_path)
26
- # test only one file
27
- mod_split = mod_abspath.split(sep)
28
- mod_split.insert(-1, "tests")
29
- mod_abspath = sep.join(mod_split)
30
- if not (os.path.exists(mod_abspath)):
31
- print("Error: no such file or directory: %s" % mod_abspath)
32
- exit(1)
33
- modules.append(mod_abspath)
34
- return modules, extra_args
35
-
36
-
37
- def nabu_test():
38
- nabu_folder = get_folder_path()
39
- args = sys.argv[1:]
40
- modules_to_test, extra_args = get_modules_to_test(args)
41
- if len(modules_to_test) == 0:
42
- modules_to_test = [
43
- nabu_folder,
44
- ]
45
- pytest_args = extra_args + modules_to_test
46
- return pytest.main(pytest_args)
47
-
48
-
49
- if __name__ == "__main__":
50
- ret = nabu_test()
51
- exit(ret)
@@ -1,375 +0,0 @@
1
- from itertools import product
2
- import tarfile
3
- import os
4
- import numpy as np
5
- from scipy.signal.windows import gaussian
6
- from silx.resources import ExternalResources
7
- from silx.io.dictdump import dicttoh5, nxtodict, dicttonx
8
- from silx.io.url import DataUrl
9
- from tomoscan.io import HDF5File
10
- from .io.utils import get_compacted_dataslices
11
-
12
- utilstest = ExternalResources(
13
- project="nabu", url_base="http://www.silx.org/pub/nabu/data/", env_key="NABU_DATA", timeout=60
14
- )
15
-
16
- __big_testdata_dir__ = os.environ.get("NABU_BIGDATA_DIR")
17
- if __big_testdata_dir__ is None or not (os.path.isdir(__big_testdata_dir__)):
18
- __big_testdata_dir__ = None
19
-
20
- __do_long_tests__ = os.environ.get("NABU_LONG_TESTS", False)
21
- if __do_long_tests__:
22
- try:
23
- __do_long_tests__ = bool(int(__do_long_tests__))
24
- except:
25
- __do_long_tests__ = False
26
-
27
- __do_large_mem_tests__ = os.environ.get("NABU_LARGE_MEM_TESTS", False)
28
- if __do_large_mem_tests__:
29
- try:
30
- __do_large_mem_tests__ = bool(int(__do_large_mem_tests__))
31
- except:
32
- __do_large_mem_tests__ = False
33
-
34
-
35
- def generate_tests_scenarios(configurations):
36
- """
37
- Generate "scenarios" of tests.
38
-
39
- The parameter is a dictionary where:
40
- - the key is the name of a parameter
41
- - the value is a list of possible parameters
42
-
43
- This function returns a list of dictionary where:
44
- - the key is the name of a parameter
45
- - the value is one value of this parameter
46
- """
47
- scenarios = [{key: val for key, val in zip(configurations.keys(), p_)} for p_ in product(*configurations.values())]
48
- return scenarios
49
-
50
-
51
- def get_data(*dataset_path):
52
- """
53
- Get a dataset file from silx.org/pub/nabu/data
54
- dataset_args is a list describing a nested folder structures, ex.
55
- ["path", "to", "my", "dataset.h5"]
56
- """
57
- dataset_relpath = os.path.join(*dataset_path)
58
- dataset_downloaded_path = utilstest.getfile(dataset_relpath)
59
- return np.load(dataset_downloaded_path)
60
-
61
-
62
- def get_array_of_given_shape(img, shape, dtype):
63
- """
64
- From a given image, returns an array of the wanted shape and dtype.
65
- """
66
-
67
- # Tile image until it's big enough.
68
- # "fun" fact: using any(blabla) crashes but using any([blabla]) does not, because of variables re-evaluation
69
- while any([i_dim <= s_dim for i_dim, s_dim in zip(img.shape, shape)]):
70
- img = np.tile(img, (2, 2))
71
- if len(shape) == 1:
72
- arr = img[: shape[0], 0]
73
- elif len(shape) == 2:
74
- arr = img[: shape[0], : shape[1]]
75
- else:
76
- arr = np.tile(img, (shape[0], 1, 1))[: shape[0], : shape[1], : shape[2]]
77
- return np.ascontiguousarray(np.squeeze(arr), dtype=dtype)
78
-
79
-
80
- def get_big_data(filename):
81
- if __big_testdata_dir__ is None:
82
- return None
83
- return np.load(os.path.join(__big_testdata_dir__, filename))
84
-
85
-
86
- def uncompress_file(compressed_file_path, target_directory):
87
- with tarfile.open(compressed_file_path) as f:
88
- f.extractall(path=target_directory)
89
-
90
-
91
- def get_file(fname):
92
- downloaded_file = dataset_downloaded_path = utilstest.getfile(fname)
93
- if ".tar" in fname:
94
- uncompress_file(downloaded_file, os.path.dirname(downloaded_file))
95
- downloaded_file = downloaded_file.split(".tar")[0]
96
- return downloaded_file
97
-
98
-
99
- def compare_arrays(arr1, arr2, tol, diff=None, absolute_value=True, percent=None, method="max", return_residual=False):
100
- """
101
- Utility to compare two arrays.
102
-
103
- Parameters
104
- ----------
105
- arr1: numpy.ndarray
106
- First array to compare
107
- arr2: numpy.ndarray
108
- Second array to compare
109
- tol: float
110
- Tolerance indicating whether arrays are close to eachother.
111
- diff: numpy.ndarray, optional
112
- Difference `arr1 - arr2`. If provided, this array is taken instead of `arr1`
113
- and `arr2`.
114
- absolute_value: bool, optional
115
- Whether to take absolute value of the difference.
116
- percent: float
117
- If set, a "relative" comparison is performed instead of a subtraction:
118
- `red(|arr1 - arr2|) / (red(|arr1|) * percent) < tol`
119
- where "red" is the reduction method (mean, max or median).
120
- method:
121
- Reduction method. Can be "max", "mean", or "median".
122
-
123
- Returns
124
- --------
125
- (is_close, residual) if return_residual is set to True
126
- is_close otherwise
127
-
128
- Examples
129
- --------
130
- When using method="mean" and absolute_value=True, this function computes
131
- the Mean Absolute Difference (MAD) metric.
132
- When also using percent=1.0, this computes the Relative Mean Absolute Difference
133
- (RMD) metric.
134
- """
135
- reductions = {
136
- "max": np.max,
137
- "mean": np.mean,
138
- "median": np.median,
139
- }
140
- if method not in reductions:
141
- raise ValueError("reduction method should be in %s" % str(list(reductions.keys())))
142
- if diff is None:
143
- diff = arr1 - arr2
144
- if absolute_value is not None:
145
- diff = np.abs(diff)
146
- residual = reductions[method](diff)
147
- if percent is not None:
148
- a1 = np.abs(arr1) if absolute_value else arr1
149
- residual /= reductions[method](a1)
150
-
151
- res = residual < tol
152
- if return_residual:
153
- res = res, residual
154
- return res
155
-
156
-
157
- def gaussian_apodization_window(shape, fwhm_ratio=0.7):
158
- fwhm = fwhm_ratio * np.array(shape)
159
- sigma = fwhm / 2.355
160
- return np.outer(*[gaussian(n, s) for n, s in zip(shape, sigma)])
161
-
162
-
163
- def compare_shifted_images(img1, img2, fwhm_ratio=0.7, return_upper_bound=False):
164
- """
165
- Compare two images that are slightly shifted from one another.
166
- Typically, tomography reconstruction wight slightly different CoR.
167
- Each image is Fourier-transformed, and the modulus is taken to get rid of the shift between the images.
168
- An apodization is done to filter the high frequencies that are usually less relevant.
169
-
170
- Parameters
171
- ----------
172
- img1: numpy.ndarray
173
- First image
174
- img2: numpy.ndarray
175
- Second image
176
- fwhm_ratio: float, optional
177
- Ratio defining the apodization in the frequency domain.
178
- A small value (eg. 0.2) means that essentually only the low frequencies will be compared.
179
- A value of 1.0 means no apodization
180
- return_upper_bound: bool, optional
181
- Whether to return a (coarse) upper bound of the comparison metric
182
-
183
- Notes
184
- -----
185
- This function roughly computes
186
- |phi(F(img1)) - phi(F(img2))|
187
- where F is the absolute value of the Fourier transform, and phi some shrinking function (here arcsinh).
188
- """
189
-
190
- def _fourier_transform(img):
191
- return np.arcsinh(np.abs(np.fft.fftshift(np.fft.fft2(img))))
192
-
193
- diff = _fourier_transform(img1) - _fourier_transform(img2)
194
- diff *= gaussian_apodization_window(img1.shape, fwhm_ratio=fwhm_ratio)
195
- res = np.abs(diff).max()
196
- if return_upper_bound:
197
- data_range = np.max(np.abs(img1))
198
- return res, np.arcsinh(np.prod(img1.shape) * data_range)
199
- else:
200
- return res
201
-
202
-
203
- class SimpleHDF5TomoScanMock:
204
- def __init__(self, image_key):
205
- self._image_key = image_key
206
-
207
- @property
208
- def image_key(self):
209
- return self._image_key
210
-
211
- @image_key.setter
212
- def image_key(self, image_key):
213
- self._image_key = image_key
214
-
215
- def save_reduced_flats(self, *args, **kwargs):
216
- pass
217
-
218
- def save_reduced_darks(self, *args, **kwargs):
219
- pass
220
-
221
-
222
- class NXDatasetMock:
223
- """
224
- An alternative to tomoscan.esrf.mock.MockHDF5, with a different interface.
225
- Attributes are not supported !
226
- """
227
-
228
- def __init__(self, data_volume, image_keys, rotation_angles=None, incident_energy=19.0, other_params=None):
229
- self.data_volume = data_volume
230
- self.n_proj = data_volume.shape[0]
231
- self.image_key = image_keys
232
- if rotation_angles is None:
233
- rotation_angles = np.linspace(0, 180, self.n_proj, False)
234
- self.rotation_angle = rotation_angles
235
- self.incident_energy = incident_energy
236
- assert image_keys.size == self.n_proj
237
- self._finalize_init(other_params)
238
- self.dataset_dict = None
239
- self.fname = None
240
- # Mocks more attributes
241
- self.dataset_scanner = SimpleHDF5TomoScanMock(image_key=self.image_key)
242
- self.kind = "hdf5"
243
-
244
- def _finalize_init(self, other_params):
245
- if other_params is None:
246
- other_params = {}
247
- default_params = {
248
- "detector": {
249
- "count_time": 0.05 * np.ones(self.n_proj, dtype="f"),
250
- "distance": 0.5,
251
- "field_of_view": "Full",
252
- "image_key_control": np.copy(self.image_key),
253
- "x_pixel_size": 6.5e-6,
254
- "y_pixel_size": 6.5e-6,
255
- "x_magnified_pixel_size": 6.5e-5,
256
- "y_magnified_pixel_size": 6.5e-5,
257
- },
258
- "sample": {
259
- "name": "dummy sample",
260
- "x_translation": 5e-4 * np.ones(self.n_proj, dtype="f"),
261
- "y_translation": 5e-4 * np.ones(self.n_proj, dtype="f"),
262
- "z_translation": 5e-4 * np.ones(self.n_proj, dtype="f"),
263
- },
264
- }
265
- default_params.update(other_params)
266
- self.other_params = default_params
267
-
268
- def generate_dict(self):
269
- beam_group = {
270
- "incident_energy": self.incident_energy,
271
- }
272
- detector_other_params = self.other_params["detector"]
273
- detector_group = {
274
- "count_time": detector_other_params["count_time"],
275
- "data": self.data_volume,
276
- "distance": detector_other_params["distance"],
277
- "field_of_view": detector_other_params["field_of_view"],
278
- "image_key": self.image_key,
279
- "image_key_control": detector_other_params["image_key_control"],
280
- "x_pixel_size": detector_other_params["x_pixel_size"],
281
- "y_pixel_size": detector_other_params["y_pixel_size"],
282
- "x_magnified_pixel_size": detector_other_params["x_magnified_pixel_size"],
283
- "y_magnified_pixel_size": detector_other_params["y_magnified_pixel_size"],
284
- }
285
- sample_other_params = self.other_params["sample"]
286
- sample_group = {
287
- "name": sample_other_params["name"],
288
- "rotation_angle": self.rotation_angle,
289
- "x_translation": sample_other_params["x_translation"],
290
- "y_translation": sample_other_params["y_translation"],
291
- "z_translation": sample_other_params["z_translation"],
292
- }
293
- self.dataset_dict = {
294
- "beam": beam_group,
295
- "instrument": {
296
- "detector": detector_group,
297
- },
298
- "sample": sample_group,
299
- }
300
-
301
- def generate_hdf5_file(self, fname, h5path=None):
302
- self.fname = fname
303
- h5path = h5path or "/entry"
304
- if self.dataset_dict is None:
305
- self.generate_dict()
306
- dicttoh5(self.dataset_dict, fname, h5path=h5path, mode="a")
307
- # Patch the "data" field which is exported as string by dicttoh5 (?!)
308
- self.dataset_path = os.path.join(h5path, "instrument/detector/data")
309
- with HDF5File(fname, "a") as fid:
310
- del fid[self.dataset_path]
311
- fid[self.dataset_path] = self.dataset_dict["instrument"]["detector"]["data"]
312
-
313
- # Mock some of the HDF5DatasetAnalyzer attributes
314
- @property
315
- def dataset_hdf5_url(self):
316
- if self.fname is None:
317
- raise ValueError("generate_hdf5_file() was not called")
318
- return DataUrl(file_path=self.fname, data_path=self.dataset_path, scheme="silx")
319
-
320
- def _get_images_with_key(self, key):
321
- indices = np.arange(self.image_key.size)[self.image_key == key]
322
- urls = [
323
- DataUrl(
324
- file_path=self.fname,
325
- data_path=self.dataset_path,
326
- data_slice=slice(img_idx, img_idx + 1),
327
- scheme="silx",
328
- )
329
- for img_idx in indices
330
- ]
331
- return dict(zip(indices, urls))
332
-
333
- @property
334
- def flats(self):
335
- return self._get_images_with_key(1)
336
-
337
- @property
338
- def darks(self):
339
- return self._get_images_with_key(2)
340
-
341
- def get_data_slices(self, what):
342
- images = getattr(self, what)
343
- # we can't directly use set() on slice() object (unhashable). Use tuples
344
- tuples_list = list(
345
- set((du.data_slice().start, du.data_slice().stop) for du in get_compacted_dataslices(images).values())
346
- )
347
- slices_list = [slice(item[0], item[1]) for item in tuples_list]
348
- return slices_list
349
-
350
-
351
- # To be improved
352
- def generate_nx_dataset(out_fname, image_key, data_volume=None, rotation_angle=None):
353
- nx_template_file = get_file("dummy.nx.tar.gz")
354
- nx_dict = nxtodict(nx_template_file)
355
- nx_entry = nx_dict["entry"]
356
-
357
- def _get_field(dict_, path):
358
- if path.startswith("/"):
359
- path = path[1:]
360
- if path.endswith("/"):
361
- path = path[:-1]
362
- split_path = path.split("/")
363
- if len(split_path) == 1:
364
- return dict_[split_path[0]]
365
- return _get_field(dict_[split_path[0]], "/".join(split_path[1:]))
366
-
367
- for name in ["image_key", "image_key_control"]:
368
- nx_entry["data"][name] = image_key
369
- nx_entry["instrument"]["detector"][name] = image_key
370
-
371
- if rotation_angle is not None:
372
- nx_entry["data"]["rotation_angle"] = rotation_angle
373
- nx_entry["sample"]["rotation_angle"] = rotation_angle
374
-
375
- dicttonx(nx_dict, out_fname)
File without changes