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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  1977. build/lib/nabu/preproc/double_flatfield_variable_region.py +0 -68
  1978. build/lib/nabu/preproc/flatfield.py +0 -448
  1979. build/lib/nabu/preproc/flatfield_cuda.py +0 -144
  1980. build/lib/nabu/preproc/flatfield_variable_region.py +0 -79
  1981. build/lib/nabu/preproc/phase.py +0 -425
  1982. build/lib/nabu/preproc/phase_cuda.py +0 -143
  1983. build/lib/nabu/preproc/shift.py +0 -95
  1984. build/lib/nabu/preproc/shift_cuda.py +0 -102
  1985. build/lib/nabu/preproc/tests/__init__.py +0 -1
  1986. build/lib/nabu/preproc/tests/test_ccd_corr.py +0 -59
  1987. build/lib/nabu/preproc/tests/test_ctf.py +0 -250
  1988. build/lib/nabu/preproc/tests/test_double_flatfield.py +0 -86
  1989. build/lib/nabu/preproc/tests/test_flatfield.py +0 -626
  1990. build/lib/nabu/preproc/tests/test_paganin.py +0 -67
  1991. build/lib/nabu/preproc/tests/test_vshift.py +0 -73
  1992. build/lib/nabu/processing/__init__.py +0 -0
  1993. build/lib/nabu/processing/convolution_cuda.py +0 -375
  1994. build/lib/nabu/processing/fft_base.py +0 -163
  1995. build/lib/nabu/processing/fft_cuda.py +0 -256
  1996. build/lib/nabu/processing/fft_opencl.py +0 -54
  1997. build/lib/nabu/processing/fftshift.py +0 -134
  1998. build/lib/nabu/processing/histogram.py +0 -286
  1999. build/lib/nabu/processing/histogram_cuda.py +0 -103
  2000. build/lib/nabu/processing/kernel_base.py +0 -126
  2001. build/lib/nabu/processing/medfilt_cuda.py +0 -159
  2002. build/lib/nabu/processing/muladd.py +0 -29
  2003. build/lib/nabu/processing/muladd_cuda.py +0 -68
  2004. build/lib/nabu/processing/padding_base.py +0 -71
  2005. build/lib/nabu/processing/padding_cuda.py +0 -75
  2006. build/lib/nabu/processing/padding_opencl.py +0 -77
  2007. build/lib/nabu/processing/processing_base.py +0 -123
  2008. build/lib/nabu/processing/roll_opencl.py +0 -64
  2009. build/lib/nabu/processing/rotation.py +0 -63
  2010. build/lib/nabu/processing/rotation_cuda.py +0 -66
  2011. build/lib/nabu/processing/tests/__init__.py +0 -0
  2012. build/lib/nabu/processing/tests/test_fft.py +0 -268
  2013. build/lib/nabu/processing/tests/test_fftshift.py +0 -71
  2014. build/lib/nabu/processing/tests/test_histogram.py +0 -55
  2015. build/lib/nabu/processing/tests/test_medfilt.py +0 -77
  2016. build/lib/nabu/processing/tests/test_muladd.py +0 -54
  2017. build/lib/nabu/processing/tests/test_padding.py +0 -247
  2018. build/lib/nabu/processing/tests/test_roll.py +0 -63
  2019. build/lib/nabu/processing/tests/test_rotation.py +0 -83
  2020. build/lib/nabu/processing/tests/test_transpose.py +0 -72
  2021. build/lib/nabu/processing/tests/test_unsharp.py +0 -106
  2022. build/lib/nabu/processing/transpose.py +0 -126
  2023. build/lib/nabu/processing/unsharp.py +0 -79
  2024. build/lib/nabu/processing/unsharp_cuda.py +0 -53
  2025. build/lib/nabu/processing/unsharp_opencl.py +0 -75
  2026. build/lib/nabu/reconstruction/__init__.py +0 -3
  2027. build/lib/nabu/reconstruction/cone.py +0 -241
  2028. build/lib/nabu/reconstruction/fbp.py +0 -124
  2029. build/lib/nabu/reconstruction/fbp_base.py +0 -391
  2030. build/lib/nabu/reconstruction/fbp_opencl.py +0 -78
  2031. build/lib/nabu/reconstruction/filtering.py +0 -220
  2032. build/lib/nabu/reconstruction/filtering_cuda.py +0 -103
  2033. build/lib/nabu/reconstruction/filtering_opencl.py +0 -111
  2034. build/lib/nabu/reconstruction/projection.py +0 -240
  2035. build/lib/nabu/reconstruction/reconstructor.py +0 -174
  2036. build/lib/nabu/reconstruction/reconstructor_cuda.py +0 -44
  2037. build/lib/nabu/reconstruction/rings.py +0 -248
  2038. build/lib/nabu/reconstruction/rings_cuda.py +0 -322
  2039. build/lib/nabu/reconstruction/sinogram.py +0 -467
  2040. build/lib/nabu/reconstruction/sinogram_cuda.py +0 -250
  2041. build/lib/nabu/reconstruction/sinogram_opencl.py +0 -40
  2042. build/lib/nabu/reconstruction/tests/__init__.py +0 -1
  2043. build/lib/nabu/reconstruction/tests/test_cone.py +0 -308
  2044. build/lib/nabu/reconstruction/tests/test_deringer.py +0 -220
  2045. build/lib/nabu/reconstruction/tests/test_fbp.py +0 -252
  2046. build/lib/nabu/reconstruction/tests/test_filtering.py +0 -133
  2047. build/lib/nabu/reconstruction/tests/test_halftomo.py +0 -100
  2048. build/lib/nabu/reconstruction/tests/test_projector.py +0 -164
  2049. build/lib/nabu/reconstruction/tests/test_reconstructor.py +0 -93
  2050. build/lib/nabu/reconstruction/tests/test_sino_normalization.py +0 -85
  2051. build/lib/nabu/resources/__init__.py +0 -0
  2052. build/lib/nabu/resources/cli/__init__.py +0 -0
  2053. build/lib/nabu/resources/cor.py +0 -5
  2054. build/lib/nabu/resources/dataset_analyzer.py +0 -469
  2055. build/lib/nabu/resources/gpu.py +0 -169
  2056. build/lib/nabu/resources/logger.py +0 -130
  2057. build/lib/nabu/resources/nxflatfield.py +0 -217
  2058. build/lib/nabu/resources/templates/__init__.py +0 -0
  2059. build/lib/nabu/resources/tests/__init__.py +0 -0
  2060. build/lib/nabu/resources/tests/test_nxflatfield.py +0 -104
  2061. build/lib/nabu/resources/tests/test_units.py +0 -47
  2062. build/lib/nabu/resources/utils.py +0 -174
  2063. build/lib/nabu/stitching/__init__.py +0 -0
  2064. build/lib/nabu/stitching/alignment.py +0 -184
  2065. build/lib/nabu/stitching/config.py +0 -1286
  2066. build/lib/nabu/stitching/definitions.py +0 -6
  2067. build/lib/nabu/stitching/frame_composition.py +0 -155
  2068. build/lib/nabu/stitching/overlap.py +0 -373
  2069. build/lib/nabu/stitching/sample_normalization.py +0 -60
  2070. build/lib/nabu/stitching/slurm_utils.py +0 -204
  2071. build/lib/nabu/stitching/tests/__init__.py +0 -0
  2072. build/lib/nabu/stitching/tests/test_alignment.py +0 -99
  2073. build/lib/nabu/stitching/tests/test_config.py +0 -226
  2074. build/lib/nabu/stitching/tests/test_frame_composition.py +0 -180
  2075. build/lib/nabu/stitching/tests/test_overlap.py +0 -98
  2076. build/lib/nabu/stitching/tests/test_sample_normalization.py +0 -49
  2077. build/lib/nabu/stitching/tests/test_slurm_utils.py +0 -146
  2078. build/lib/nabu/stitching/tests/test_utils.py +0 -21
  2079. build/lib/nabu/stitching/tests/test_z_stitching.py +0 -1183
  2080. build/lib/nabu/stitching/utils.py +0 -563
  2081. build/lib/nabu/stitching/z_stitching.py +0 -2279
  2082. build/lib/nabu/tests.py +0 -51
  2083. build/lib/nabu/testutils.py +0 -375
  2084. build/lib/nabu/thirdparty/__init__.py +0 -0
  2085. build/lib/nabu/thirdparty/algotom_convert_sino.py +0 -276
  2086. build/lib/nabu/thirdparty/pore3d_deringer_munch.py +0 -108
  2087. build/lib/nabu/thirdparty/tomocupy_remove_stripe.py +0 -586
  2088. build/lib/nabu/thirdparty/tomopy_phase.py +0 -239
  2089. build/lib/nabu/thirdparty/tomwer_load_flats_darks.py +0 -162
  2090. build/lib/nabu/utils.py +0 -836
  2091. nabu-2024.1.1.dist-info/RECORD +0 -2375
  2092. nabu-2024.1.1.dist-info/top_level.txt +0 -4
  2093. {build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app → nabu/app/tests}/__init__.py +0 -0
  2094. {nabu-2024.1.1.dist-info → nabu-2024.1.2.dist-info}/LICENSE +0 -0
  2095. {nabu-2024.1.1.dist-info → nabu-2024.1.2.dist-info}/entry_points.txt +0 -0
@@ -1,116 +0,0 @@
1
- from ..utils import deprecated_class
2
- from .config_validators import str2bool
3
- from dataclasses import dataclass
4
- import os
5
-
6
- #
7
- # Decorators and callback mechanism
8
- #
9
-
10
-
11
- def use_options(step_name, step_attr):
12
- def decorator(func):
13
- def wrapper(*args, **kwargs):
14
- self = args[0]
15
- if step_name not in self.processing_steps:
16
- self.__setattr__(step_attr, None)
17
- return
18
- self._steps_name2component[step_name] = step_attr
19
- self._steps_component2name[step_attr] = step_name
20
- return func(*args, **kwargs)
21
-
22
- return wrapper
23
-
24
- return decorator
25
-
26
-
27
- def pipeline_step(step_attr, step_desc):
28
- def decorator(func):
29
- def wrapper(*args, **kwargs):
30
- self = args[0]
31
- if self.__getattribute__(step_attr) is None:
32
- return
33
- self.logger.info(step_desc)
34
- res = func(*args, **kwargs)
35
- step_name = self._steps_component2name[step_attr]
36
- callbacks = self._callbacks.get(step_name, None)
37
- if callbacks is not None:
38
- for callback in callbacks:
39
- callback(self)
40
- if self.datadump_manager is not None and step_name in self.datadump_manager.data_dump:
41
- self.datadump_manager.dump_data_to_file(step_name, self.radios)
42
- return res
43
-
44
- return wrapper
45
-
46
- return decorator
47
-
48
-
49
- #
50
- # sub-region, shapes, etc
51
- #
52
-
53
-
54
- def get_subregion(sub_region, ndim=3):
55
- """
56
- Return a "normalized" sub-region in the form ((start_z, end_z), (start_y, end_y), (start_x, end_x)).
57
-
58
- Parameters
59
- ----------
60
- sub_region: tuple
61
- A tuple of tuples or tuple of integers.
62
-
63
- Notes
64
- -----
65
- The parameter "sub_region" is normally a tuple of tuples of integers.
66
- However it can be more convenient to use tuple of integers.
67
- This function will attempt at catching the different cases, but will fail if
68
- 'sub_region' contains heterogeneous types (ex. tuples along with int)
69
- """
70
- if sub_region is None:
71
- res = ((None, None),)
72
- elif hasattr(sub_region[0], "__iter__"):
73
- if set(map(len, sub_region)) != set([2]):
74
- raise ValueError("Expected each tuple to be in the form (start, end)")
75
- res = sub_region
76
- else:
77
- if len(sub_region) % 2:
78
- raise ValueError("Expected even number of elements")
79
- starts, ends = sub_region[::2], sub_region[1::2]
80
- res = tuple([(s, e) for s, e in zip(starts, ends)])
81
- if len(res) != ndim:
82
- res += ((None, None),) * (ndim - len(res))
83
- return res
84
-
85
-
86
- #
87
- # Writer - moved to pipeline.writer
88
- #
89
-
90
- from .writer import WriterManager
91
-
92
- WriterConfigurator = deprecated_class("WriterConfigurator moved to nabu.pipeline.writer.WriterManager", do_print=True)(
93
- WriterManager
94
- )
95
-
96
-
97
- @dataclass
98
- class EnvSettings:
99
- """This class centralises the definitions, possibly documentation, and access to environnt variable
100
- driven settings.
101
- It is meant to be used in the following way:
102
- from nabu.utils import nabu_env_settings
103
- if not nabu_env_settings.skip_tomoscan_checks:
104
- do something
105
- """
106
-
107
- skip_tomoscan_checks: bool = False
108
-
109
-
110
- def _get_nabu_environment_variables():
111
- nabu_env_settings = EnvSettings()
112
- nabu_env_settings.skip_tomoscan_checks = str2bool(os.getenv("SKIP_TOMOSCAN_CHECK", "0"))
113
- return nabu_env_settings
114
-
115
-
116
- nabu_env_settings = _get_nabu_environment_variables()
@@ -1,193 +0,0 @@
1
- from os import path
2
- from tomoscan.esrf import TIFFVolume, MultiTIFFVolume, EDFVolume, JP2KVolume
3
- from ..utils import check_supported, get_num_threads
4
- from ..resources.logger import LoggerOrPrint
5
- from ..io.writer import NXProcessWriter, HSTVolVolume, NXVolVolume
6
- from ..io.utils import convert_dict_values
7
- from .params import files_formats
8
-
9
-
10
- class WriterManager:
11
-
12
- """
13
- This class is a wrapper on top of all "writers".
14
- It will create the right "writer" with all the necessary options, and the histogram writer.
15
-
16
- The layout is the following.
17
-
18
- * Single-big-file volume formats (big-tiff, .vol):
19
- - no start index
20
- - everything is increasingly written in one file
21
- * Multiple-frames per file (HDF5 + master-file):
22
- - needs a start index (change file_prefix) for each partial file
23
- - needs a subdirectory for partial files
24
- * One-file-per-frame (tiff, edf, jp2)
25
- - start_index
26
-
27
- When saving intermediate steps (eg. sinogram): HDF5 format is always used.
28
- """
29
-
30
- _overwrite_warned = False
31
- _writer_classes = {
32
- "hdf5": NXVolVolume,
33
- "tiff": TIFFVolume,
34
- "bigtiff": MultiTIFFVolume,
35
- "jp2": JP2KVolume,
36
- "edf": EDFVolume,
37
- "vol": HSTVolVolume,
38
- }
39
-
40
- def __init__(
41
- self,
42
- output_dir,
43
- file_prefix,
44
- file_format="hdf5",
45
- overwrite=False,
46
- start_index=0,
47
- logger=None,
48
- metadata=None,
49
- histogram=False,
50
- extra_options=None,
51
- ):
52
- """
53
- Create a Writer from a set of parameters.
54
-
55
- Parameters
56
- ----------
57
- output_dir: str
58
- Directory where the file(s) will be written.
59
- file_prefix: str
60
- File prefix (without leading path)
61
- start_index: int, optional
62
- Index to start the files numbering (filename_0123.ext).
63
- Default is 0.
64
- Ignored for HDF5 extension.
65
- logger: nabu.resources.logger.Logger, optional
66
- Logger object
67
- metadata: dict, optional
68
- Metadata, eg. information on various processing steps. For HDF5, it will go to "configuration"
69
- histogram: bool, optional
70
- Whether to also write a histogram of data. If set to True, it will configure
71
- an additional "writer".
72
- extra_options: dict, optional
73
- Other advanced options to pass to Writer class.
74
- """
75
- self.extra_options = extra_options or {}
76
- self._set_file_format(file_format)
77
- self.overwrite = overwrite
78
- self.start_index = start_index
79
- self.logger = LoggerOrPrint(logger)
80
- self.histogram = histogram
81
- self.output_dir = output_dir
82
- self.file_prefix = file_prefix
83
- self.metadata = convert_dict_values(metadata or {}, {None: "None"})
84
- self._init_writer()
85
- self._init_histogram_writer()
86
-
87
- def _set_file_format(self, file_format):
88
- check_supported(file_format, files_formats, "file format")
89
- self.file_format = files_formats[file_format]
90
- self._is_bigtiff = file_format in ["tiff", "tif"] and any(
91
- [self.extra_options.get(opt, False) for opt in ["tiff_single_file", "use_bigtiff"]]
92
- )
93
- if self._is_bigtiff:
94
- self.file_format = "bigtiff"
95
-
96
- @staticmethod
97
- def get_first_fname(vol_writer):
98
- if hasattr(vol_writer, "file_path"):
99
- return path.dirname(vol_writer.file_path)
100
- dirname = vol_writer.data_url.file_path()
101
- fname = vol_writer.data_url.data_path().format(
102
- volume_basename=vol_writer._volume_basename,
103
- index_zfill6=vol_writer.start_index,
104
- data_extension=vol_writer.extension or vol_writer.DEFAULT_DATA_EXTENSION,
105
- )
106
- return path.join(dirname, fname)
107
-
108
- @staticmethod
109
- def get_fname(vol_writer):
110
- if hasattr(vol_writer, "file_path"):
111
- # several frames per file - return the file itself
112
- return vol_writer.file_path
113
- # one file per frame - return the directory
114
- return vol_writer.data_url.file_path()
115
-
116
- def _init_writer(self):
117
- if self.file_format in ["tiff", "edf", "jp2", "hdf5"]:
118
- writer_kwargs = {
119
- "folder": self.output_dir,
120
- "volume_basename": self.file_prefix,
121
- "start_index": self.start_index,
122
- "overwrite": self.overwrite,
123
- }
124
- if self.file_format == "hdf5":
125
- writer_kwargs["data_path"] = self.metadata.get("entry", "entry")
126
- writer_kwargs["process_name"] = self.metadata.get("process_name", "reconstruction")
127
- writer_kwargs["create_subfolder"] = self.extra_options.get("create_subfolder", True)
128
- elif self.file_format == "jp2":
129
- writer_kwargs["cratios"] = self.metadata.get("jpeg2000_compression_ratio", None)
130
- writer_kwargs["clip_values"] = self.metadata.get("float_clip_values", None)
131
- writer_kwargs["n_threads"] = get_num_threads()
132
- elif self.file_format in ["vol", "bigtiff"]:
133
- writer_kwargs = {
134
- "file_path": path.join(
135
- self.output_dir, self.file_prefix + "." + self.file_format.replace("bigtiff", "tiff")
136
- ),
137
- "overwrite": self.overwrite,
138
- "append": self.extra_options.get("single_output_file_initialized", False),
139
- "hst_metadata": self.extra_options.get("raw_vol_metadata", {}),
140
- }
141
- else:
142
- raise ValueError("Unsupported file format: %s" % self.file_format)
143
- self._h5_entry = self.metadata.get("entry", "entry")
144
- self.writer = self._writer_classes[self.file_format](**writer_kwargs)
145
- self.fname = self.get_fname(self.writer)
146
- if path.exists(self.fname):
147
- err = "File already exists: %s" % self.fname
148
- if self.overwrite:
149
- if not (self.__class__._overwrite_warned):
150
- self.logger.warning(err + ". It will be overwritten as requested in configuration")
151
- self.__class__._overwrite_warned = True
152
- else:
153
- self.logger.fatal(err)
154
- raise ValueError(err)
155
-
156
- def _init_histogram_writer(self):
157
- if not self.histogram:
158
- return
159
- separate_histogram_file = not (self.file_format == "hdf5")
160
- if separate_histogram_file:
161
- fmode = "w"
162
- hist_fname = path.join(self.output_dir, "histogram_%05d.hdf5" % self.start_index)
163
- else:
164
- fmode = "a"
165
- hist_fname = self.fname
166
- # Nabu's original NXProcessWriter has to be used here, as histogram is not 3D
167
- self.histogram_writer = NXProcessWriter(
168
- hist_fname,
169
- entry=self._h5_entry,
170
- filemode=fmode,
171
- overwrite=True,
172
- )
173
-
174
- def write_histogram(self, data, config=None, processing_index=1):
175
- if not (self.histogram):
176
- return
177
- self.histogram_writer.write(
178
- data,
179
- "histogram",
180
- processing_index=processing_index,
181
- config=config,
182
- is_frames_stack=False,
183
- direct_access=False,
184
- )
185
-
186
- def _write_metadata(self):
187
- self.writer.metadata = self.metadata
188
- self.writer.save_metadata()
189
-
190
- def write_data(self, data):
191
- self.writer.data = data
192
- self.writer.save()
193
- # self._write_metadata()
File without changes
@@ -1,7 +0,0 @@
1
- from .ccd import CCDFilter, Log
2
- from .ctf import CTFPhaseRetrieval
3
- from .distortion import DistortionCorrection
4
- from .double_flatfield import DoubleFlatField
5
- from .flatfield import FlatField, FlatFieldDataUrls
6
- from .phase import PaganinPhaseRetrieval
7
- from .shift import VerticalShift
@@ -1,11 +0,0 @@
1
- # Backward compat.
2
- from ..estimation.alignment import AlignmentBase
3
- from ..estimation.cor import (
4
- CenterOfRotation,
5
- CenterOfRotationAdaptiveSearch,
6
- CenterOfRotationGrowingWindow,
7
- CenterOfRotationSlidingWindow,
8
- )
9
- from ..estimation.translation import DetectorTranslationAlongBeam
10
- from ..estimation.focus import CameraFocus
11
- from ..estimation.tilt import CameraTilt
@@ -1,161 +0,0 @@
1
- import numpy as np
2
- from ..utils import check_supported
3
- from silx.math.medianfilter import medfilt2d
4
-
5
-
6
- class CCDFilter:
7
- """
8
- Filtering applied on radios.
9
- """
10
-
11
- _supported_ccd_corrections = ["median_clip"]
12
-
13
- def __init__(
14
- self,
15
- radios_shape: tuple,
16
- correction_type: str = "median_clip",
17
- median_clip_thresh: float = 0.1,
18
- abs_diff=False,
19
- preserve_borders=False,
20
- ):
21
- """
22
- Initialize a CCDCorrection instance.
23
-
24
- Parameters
25
- -----------
26
- radios_shape: tuple
27
- A tuple describing the shape of the radios stack, in the form
28
- `(n_radios, n_z, n_x)`.
29
- correction_type: str
30
- Correction type for radios ("median_clip", "sigma_clip", ...)
31
- median_clip_thresh: float, optional
32
- Threshold for the median clipping method.
33
- abs_diff: boolean
34
- by default False: the correction is triggered when img - median > threshold.
35
- If equals True: correction is triggered for abs(img-media) > threshold
36
- preserve borders: boolean
37
- by default False:
38
- If equals True: the borders (width=1) are not modified.
39
-
40
-
41
- Notes
42
- ------
43
- A CCD correction is a process (usually filtering) taking place in the
44
- radios space.
45
- Available filters:
46
- - median_clip: if the value of the current pixel exceeds the median
47
- of adjacent pixels (a 3x3 neighborhood) more than a threshold,
48
- then this pixel value is set to the median value.
49
- """
50
- self._set_radios_shape(radios_shape)
51
- check_supported(correction_type, self._supported_ccd_corrections, "CCD correction mode")
52
- self.correction_type = correction_type
53
- self.median_clip_thresh = median_clip_thresh
54
- self.abs_diff = abs_diff
55
- self.preserve_borders = preserve_borders
56
-
57
- def _set_radios_shape(self, radios_shape):
58
- if len(radios_shape) == 2:
59
- self.radios_shape = (1,) + radios_shape
60
- elif len(radios_shape) == 3:
61
- self.radios_shape = radios_shape
62
- else:
63
- raise ValueError("Expected radios to have 2 or 3 dimensions")
64
- n_radios, n_z, n_x = self.radios_shape
65
- self.n_radios = n_radios
66
- self.n_angles = n_radios
67
- self.shape = (n_z, n_x)
68
-
69
- @staticmethod
70
- def median_filter(img):
71
- """
72
- Perform a median filtering on an image.
73
- """
74
- return medfilt2d(img, (3, 3), mode="reflect")
75
-
76
- def median_clip_mask(self, img, return_medians=False):
77
- """
78
- Compute a mask indicating whether a pixel is valid or not, according to
79
- the median-clip method.
80
-
81
- Parameters
82
- ----------
83
- img: numpy.ndarray
84
- Input image
85
- return_medians: bool, optional
86
- Whether to return the median values additionally to the mask.
87
- """
88
- median_values = self.median_filter(img)
89
- if not self.abs_diff:
90
- invalid_mask = img >= median_values + self.median_clip_thresh
91
- else:
92
- invalid_mask = abs(img - median_values) > self.median_clip_thresh
93
-
94
- if return_medians:
95
- return invalid_mask, median_values
96
- else:
97
- return invalid_mask
98
-
99
- def median_clip_correction(self, radio, output=None):
100
- """
101
- Compute the median clip correction on one image.
102
-
103
- Parameters
104
- ----------
105
- radios: numpy.ndarray, optional
106
- A radio image.
107
- output: numpy.ndarray, optional
108
- Output array
109
- """
110
- assert radio.shape == self.shape
111
- if output is None:
112
- output = np.copy(radio)
113
- else:
114
- output[:] = radio[:]
115
- invalid_mask, medians = self.median_clip_mask(radio, return_medians=True)
116
-
117
- if self.preserve_borders:
118
- fixed_border = np.array(radio[[0, 0, -1, -1], [0, -1, 0, -1]])
119
-
120
- output[invalid_mask] = medians[invalid_mask]
121
-
122
- if self.preserve_borders:
123
- output[[0, 0, -1, -1], [0, -1, 0, -1]] = fixed_border
124
-
125
- return output
126
-
127
-
128
- class Log:
129
- """
130
- Helper class to take -log(radios)
131
-
132
- Parameters
133
- -----------
134
- clip_min: float, optional
135
- Before taking the logarithm, the values are clipped to this minimum.
136
- clip_max: float, optional
137
- Before taking the logarithm, the values are clipped to this maximum.
138
- """
139
-
140
- def __init__(self, radios_shape, clip_min=None, clip_max=None):
141
- self.radios_shape = radios_shape
142
- self.clip_min = clip_min
143
- self.clip_max = clip_max
144
-
145
- def take_logarithm(self, radios):
146
- """
147
- Take the negative logarithm of a radios chunk.
148
- Processing is done in-place !
149
-
150
- Parameters
151
- -----------
152
- radios: array
153
- Radios chunk.
154
- """
155
- if (self.clip_min is not None) or (self.clip_max is not None):
156
- np.clip(radios, self.clip_min, self.clip_max, out=radios)
157
- np.log(radios, out=radios)
158
- else:
159
- np.log(radios, out=radios)
160
- radios[:] *= -1
161
- return radios
@@ -1,169 +0,0 @@
1
- import numpy as np
2
- from ..preproc.ccd import CCDFilter, Log
3
- from ..processing.medfilt_cuda import MedianFilter
4
- from ..utils import get_cuda_srcfile, updiv, deprecated_class
5
- from ..cuda.utils import __has_pycuda__
6
-
7
- if __has_pycuda__:
8
- from ..cuda.kernel import CudaKernel
9
-
10
- # COMPAT.
11
- from .flatfield_cuda import (
12
- CudaFlatField as CudaFlatfield_,
13
- CudaFlatFieldArrays as CudaFlatFieldArrays_,
14
- CudaFlatFieldDataUrls as CudaFlatFieldDataUrls_,
15
- )
16
-
17
- FlatField = deprecated_class(
18
- "preproc.ccd_cuda.CudaFlatField was moved to preproc.flatfield_cuda.CudaFlatField", do_print=True
19
- )(CudaFlatfield_)
20
- FlatFieldArrays = deprecated_class(
21
- "preproc.ccd_cuda.CudaFlatFieldArrays was moved to preproc.flatfield_cuda.CudaFlatFieldArrays", do_print=True
22
- )(CudaFlatFieldArrays_)
23
- FlatFieldDataUrls = deprecated_class(
24
- "preproc.ccd_cuda.CudaFlatFieldDataUrls was moved to preproc.flatfield_cuda.CudaFlatFieldDataUrls", do_print=True
25
- )(CudaFlatFieldDataUrls_)
26
- #
27
-
28
-
29
- class CudaCCDFilter(CCDFilter):
30
- def __init__(
31
- self,
32
- radios_shape,
33
- correction_type="median_clip",
34
- median_clip_thresh=0.1,
35
- abs_diff=False,
36
- cuda_options=None,
37
- ):
38
- """
39
- Initialize a CudaCCDCorrection instance.
40
- Please refer to the documentation of CCDCorrection.
41
- """
42
- super().__init__(
43
- radios_shape,
44
- correction_type=correction_type,
45
- median_clip_thresh=median_clip_thresh,
46
- )
47
- self._set_cuda_options(cuda_options)
48
- self.cuda_median_filter = None
49
- if correction_type == "median_clip":
50
- self.cuda_median_filter = MedianFilter(
51
- self.shape,
52
- footprint=(3, 3),
53
- mode="reflect",
54
- threshold=median_clip_thresh,
55
- abs_diff=abs_diff,
56
- cuda_options={
57
- "device_id": self.cuda_options["device_id"],
58
- "ctx": self.cuda_options["ctx"],
59
- "cleanup_at_exit": self.cuda_options["cleanup_at_exit"],
60
- },
61
- )
62
-
63
- def _set_cuda_options(self, user_cuda_options):
64
- self.cuda_options = {"device_id": None, "ctx": None, "cleanup_at_exit": None}
65
- if user_cuda_options is None:
66
- user_cuda_options = {}
67
- self.cuda_options.update(user_cuda_options)
68
-
69
- def median_clip_correction(self, radio, output=None):
70
- """
71
- Compute the median clip correction on one image.
72
-
73
- Parameters
74
- ----------
75
- radio: pycuda.gpuarray
76
- A radio image
77
- output: pycuda.gpuarray, optional
78
- Output data.
79
- """
80
- assert radio.shape == self.shape
81
- return self.cuda_median_filter.medfilt2(radio, output=output)
82
-
83
-
84
- CudaCCDCorrection = deprecated_class("CudaCCDCorrection is replaced with CudaCCDFilter", do_print=True)(CudaCCDFilter)
85
-
86
-
87
- class CudaLog(Log):
88
- """
89
- Helper class to take -log(radios)
90
- """
91
-
92
- def __init__(self, radios_shape, clip_min=None, clip_max=None):
93
- """
94
- Initialize a Log processing.
95
-
96
- Parameters
97
- -----------
98
- radios_shape: tuple
99
- The shape of 3D radios stack.
100
- clip_min: float, optional
101
- Data smaller than this value is replaced by this value.
102
- clip_max: float, optional.
103
- Data bigger than this value is replaced by this value.
104
- """
105
- super().__init__(radios_shape, clip_min=clip_min, clip_max=clip_max)
106
- self._init_kernels()
107
-
108
- def _init_kernels(self):
109
- self._do_clip_min = int(self.clip_min is not None)
110
- self._do_clip_max = int(self.clip_max is not None)
111
- self.clip_min = np.float32(self.clip_min or 0)
112
- self.clip_max = np.float32(self.clip_max or 1)
113
- self._nlog_srcfile = get_cuda_srcfile("ElementOp.cu")
114
- nz, ny, nx = self.radios_shape
115
- self._nx = np.int32(nx)
116
- self._ny = np.int32(ny)
117
- self._nz = np.int32(nz)
118
- self._nthreadsperblock = (16, 16, 4) # TODO tune ?
119
- self._nblocks = tuple([updiv(n, p) for n, p in zip([nx, ny, nz], self._nthreadsperblock)])
120
-
121
- self.nlog_kernel = CudaKernel(
122
- "nlog",
123
- filename=self._nlog_srcfile,
124
- signature="Piiiff",
125
- options=[
126
- "-DDO_CLIP_MIN=%d" % self._do_clip_min,
127
- "-DDO_CLIP_MAX=%d" % self._do_clip_max,
128
- ],
129
- )
130
-
131
- def take_logarithm(self, radios, clip_min=None, clip_max=None):
132
- """
133
- Take the negative logarithm of a radios chunk.
134
-
135
- Parameters
136
- -----------
137
- radios: `pycuda.gpuarray.GPUArray`
138
- Radios chunk
139
- If not provided, a new GPU array is created.
140
- clip_min: float, optional
141
- Before taking the logarithm, the values are clipped to this minimum.
142
- clip_max: float, optional
143
- Before taking the logarithm, the values are clipped to this maximum.
144
- """
145
- clip_min = clip_min or self.clip_min
146
- clip_max = clip_max or self.clip_max
147
- if radios.flags.c_contiguous:
148
- self.nlog_kernel(
149
- radios,
150
- self._nx,
151
- self._ny,
152
- self._nz,
153
- clip_min,
154
- clip_max,
155
- grid=self._nblocks,
156
- block=self._nthreadsperblock,
157
- )
158
- else:
159
- # map-like operations cannot be directly applied on 3D arrays
160
- # that are not C-contiguous. We have to process image per image.
161
- # TODO it's even worse when each single frame is not C-contiguous. For now this case is not handled
162
- nz = np.int32(1)
163
- nthreadsperblock = (32, 32, 1)
164
- nblocks = tuple([updiv(n, p) for n, p in zip([int(self._nx), int(self._ny), int(nz)], nthreadsperblock)])
165
- for i in range(radios.shape[0]):
166
- self.nlog_kernel(
167
- radios[i], self._nx, self._ny, nz, clip_min, clip_max, grid=nblocks, block=nthreadsperblock
168
- )
169
- return radios