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
@@ -1,73 +0,0 @@
1
- import pytest
2
- import numpy as np
3
- from scipy.ndimage import shift as ndshift
4
- from nabu.preproc.shift import VerticalShift
5
- from nabu.cuda.utils import __has_pycuda__, get_cuda_context
6
-
7
- if __has_pycuda__:
8
- import pycuda.gpuarray as garray
9
- from nabu.preproc.shift_cuda import CudaVerticalShift
10
-
11
-
12
- @pytest.fixture(scope="class")
13
- def bootstrap(request):
14
- cls = request.cls
15
- data = np.zeros([13, 11], "f")
16
- slope = 100 + np.arange(13)
17
- data[:] = slope[:, None]
18
- cls.radios = np.array([data] * 17)
19
- cls.shifts = 0.3 + np.arange(17)
20
- cls.indexes = range(17)
21
- # given the shifts and the radios we build the golden reference
22
- golden = []
23
- for iradio in range(17):
24
- projection_number = cls.indexes[iradio]
25
- my_shift = cls.shifts[projection_number]
26
- padded_radio = np.concatenate(
27
- [cls.radios[iradio], np.zeros([1, 11], "f")], axis=0
28
- ) # needs padding because ndshifs does not work as expected
29
- shifted_padded_radio = ndshift(padded_radio, [-my_shift, 0], mode="constant", cval=0.0, order=1).astype("f")
30
- shifted_radio = shifted_padded_radio[:-1]
31
- golden.append(shifted_radio)
32
- cls.golden = np.array(golden)
33
- cls.tol = 1e-5
34
- if __has_pycuda__:
35
- cls.ctx = get_cuda_context()
36
-
37
-
38
- @pytest.mark.usefixtures("bootstrap")
39
- class TestVerticalShift:
40
- def test_vshift(self):
41
- radios = self.radios.copy()
42
- new_radios = np.zeros_like(radios)
43
-
44
- Shifter = VerticalShift(radios.shape, self.shifts)
45
-
46
- Shifter.apply_vertical_shifts(radios, self.indexes, output=new_radios)
47
- assert abs(new_radios - self.golden).max() < self.tol
48
-
49
- Shifter.apply_vertical_shifts(radios, self.indexes)
50
- assert abs(radios - self.golden).max() < self.tol
51
-
52
- @pytest.mark.skipif(not (__has_pycuda__), reason="Need cuda/pycuda for this test")
53
- def test_cuda_vshift(self):
54
- d_radios = garray.to_gpu(self.radios)
55
- d_radios2 = d_radios.copy()
56
- d_out = garray.zeros_like(d_radios)
57
-
58
- Shifter = CudaVerticalShift(d_radios.shape, self.shifts)
59
- Shifter.apply_vertical_shifts(d_radios, self.indexes, output=d_out)
60
- assert abs(d_out.get() - self.golden).max() < self.tol
61
-
62
- Shifter.apply_vertical_shifts(d_radios, self.indexes)
63
- assert abs(d_radios.get() - self.golden).max() < self.tol
64
-
65
- # Test with negative shifts
66
- radios2 = self.radios.copy()
67
- Shifter_neg = VerticalShift(self.radios.shape, -self.shifts)
68
- Shifter_neg.apply_vertical_shifts(radios2, self.indexes)
69
-
70
- Shifter_neg_cuda = CudaVerticalShift(d_radios.shape, -self.shifts)
71
- Shifter_neg_cuda.apply_vertical_shifts(d_radios2, self.indexes)
72
- err_max = np.max(np.abs(d_radios2.get() - radios2))
73
- assert err_max < 1e-6, "Something wrong for negative translations: max error = %.2e" % err_max
@@ -1,375 +0,0 @@
1
- from os.path import dirname
2
- import numpy as np
3
- from ..utils import updiv, get_cuda_srcfile
4
- from ..cuda.utils import __has_pycuda__
5
- from ..misc.utils import ConvolutionInfos
6
- from ..cuda.processing import CudaProcessing
7
-
8
- if __has_pycuda__:
9
- from pycuda.compiler import SourceModule
10
-
11
-
12
- class Convolution:
13
- """
14
- A class for performing convolution on GPU with CUDA, but without using
15
- textures (unlike for example in ``silx.opencl.convolution``)
16
- """
17
-
18
- def __init__(self, shape, kernel, axes=None, mode=None, extra_options=None, cuda_options=None):
19
- """
20
- Constructor of Cuda Convolution.
21
-
22
- Parameters
23
- -----------
24
- shape: tuple
25
- Shape of the array.
26
- kernel: array-like
27
- Convolution kernel (1D, 2D or 3D).
28
- axes: tuple, optional
29
- Axes along which the convolution is performed,
30
- for batched convolutions.
31
- mode: str, optional
32
- Boundary handling mode. Available modes are:
33
- - "reflect": cba|abcd|dcb
34
- - "nearest": aaa|abcd|ddd
35
- - "wrap": bcd|abcd|abc
36
- - "constant": 000|abcd|000
37
-
38
- Default is "reflect".
39
- extra_options: dict, optional
40
- Advanced options (dict). Current options are:
41
- - "allocate_input_array": True
42
- - "allocate_output_array": True
43
- - "allocate_tmp_array": True
44
- - "sourcemodule_kwargs": {}
45
- - "batch_along_flat_dims": True
46
- """
47
- self.cuda = CudaProcessing(**(cuda_options or {}))
48
- self._configure_extra_options(extra_options)
49
- self._determine_use_case(shape, kernel, axes)
50
- self._allocate_memory(mode)
51
- self._init_kernels()
52
-
53
- def _configure_extra_options(self, extra_options):
54
- self.extra_options = {
55
- "allocate_input_array": True,
56
- "allocate_output_array": True,
57
- "allocate_tmp_array": True,
58
- "sourcemodule_kwargs": {},
59
- "batch_along_flat_dims": True,
60
- }
61
- extra_opts = extra_options or {}
62
- self.extra_options.update(extra_opts)
63
- self.sourcemodule_kwargs = self.extra_options["sourcemodule_kwargs"]
64
-
65
- def _get_dimensions(self, shape, kernel):
66
- self.shape = shape
67
- self.data_ndim = self._check_dimensions(shape=shape, name="Data")
68
- self.kernel_ndim = self._check_dimensions(arr=kernel, name="Kernel")
69
- Nx = shape[-1]
70
- if self.data_ndim >= 2:
71
- Ny = shape[-2]
72
- else:
73
- Ny = 1
74
- if self.data_ndim >= 3:
75
- Nz = shape[-3]
76
- else:
77
- Nz = 1
78
- self.Nx = np.int32(Nx)
79
- self.Ny = np.int32(Ny)
80
- self.Nz = np.int32(Nz)
81
-
82
- def _determine_use_case(self, shape, kernel, axes):
83
- """
84
- Determine the convolution use case from the input/kernel shape, and axes.
85
- """
86
- self._get_dimensions(shape, kernel)
87
- if self.kernel_ndim > self.data_ndim:
88
- raise ValueError("Kernel dimensions cannot exceed data dimensions")
89
- data_ndim = self.data_ndim
90
- kernel_ndim = self.kernel_ndim
91
- self.kernel = kernel.astype("f")
92
-
93
- convol_infos = ConvolutionInfos()
94
- k = (data_ndim, kernel_ndim)
95
- if k not in convol_infos.use_cases:
96
- raise ValueError(
97
- "Cannot find a use case for data ndim = %d and kernel ndim = %d" % (data_ndim, kernel_ndim)
98
- )
99
- possible_use_cases = convol_infos.use_cases[k]
100
-
101
- # If some dimensions are "flat", make a batched convolution along them
102
- # Ex. data_dim = (1, Nx) -> batched 1D convolution
103
- if self.extra_options["batch_along_flat_dims"] and (1 in self.shape):
104
- axes = tuple([curr_dim for numels, curr_dim in zip(self.shape, range(len(self.shape))) if numels != 1])
105
- #
106
- self.use_case_name = None
107
- for uc_name, uc_params in possible_use_cases.items():
108
- if axes in convol_infos.allowed_axes[uc_name]:
109
- self.use_case_name = uc_name
110
- self.use_case_desc = uc_params["name"]
111
- self.use_case_kernels = uc_params["kernels"].copy()
112
- if self.use_case_name is None:
113
- raise ValueError(
114
- "Cannot find a use case for data ndim = %d, kernel ndim = %d and axes=%s"
115
- % (data_ndim, kernel_ndim, str(axes))
116
- )
117
- # TODO implement this use case
118
- if self.use_case_name == "batched_separable_2D_1D_3D":
119
- raise NotImplementedError("The use case %s is not implemented" % self.use_case_name)
120
- #
121
- self.axes = axes
122
- # Replace "axes=None" with an actual value (except for ND-ND)
123
- allowed_axes = convol_infos.allowed_axes[self.use_case_name]
124
- if len(allowed_axes) > 1:
125
- # The default choice might impact perfs
126
- self.axes = allowed_axes[0] or allowed_axes[1]
127
- self.separable = self.use_case_name.startswith("separable")
128
- self.batched = self.use_case_name.startswith("batched")
129
-
130
- def _allocate_memory(self, mode):
131
- self.mode = mode or "reflect"
132
- # The current implementation does not support kernel size bigger than data size,
133
- # except for mode="nearest"
134
- for i, dim_size in enumerate(self.shape):
135
- if min(self.kernel.shape) > dim_size and i in self.axes:
136
- print(
137
- "Warning: kernel support is too large for data dimension %d (%d). Forcing convolution mode to 'nearest'"
138
- % (i, dim_size)
139
- )
140
- self.mode = "nearest"
141
- #
142
- option_array_names = {
143
- "allocate_input_array": "data_in",
144
- "allocate_output_array": "data_out",
145
- "allocate_tmp_array": "data_tmp",
146
- }
147
- # Nonseparable transforms do not need tmp array
148
- if not (self.separable):
149
- self.extra_options["allocate_tmp_array"] = False
150
- # Allocate arrays
151
- for option_name, array_name in option_array_names.items():
152
- if self.extra_options[option_name]:
153
- value = self.cuda.allocate_array("value", self.shape, np.float32)
154
- else:
155
- value = None
156
- setattr(self, array_name, value)
157
-
158
- if isinstance(self.kernel, np.ndarray):
159
- self.d_kernel = self.cuda.to_device("d_kernel", self.kernel)
160
- else:
161
- if not (isinstance(self.kernel, self.cuda.array_class)):
162
- raise ValueError("kernel must be either numpy array or pycuda array")
163
- self.d_kernel = self.kernel
164
- self._old_input_ref = None
165
- self._old_output_ref = None
166
- self._c_modes_mapping = {
167
- "periodic": 2,
168
- "wrap": 2,
169
- "nearest": 1,
170
- "replicate": 1,
171
- "reflect": 0,
172
- "constant": 3,
173
- }
174
- mp = self._c_modes_mapping
175
- if self.mode.lower() not in mp:
176
- raise ValueError(
177
- """
178
- Mode %s is not available. Available modes are:
179
- %s
180
- """
181
- % (self.mode, str(mp.keys()))
182
- )
183
- if self.mode.lower() == "constant":
184
- raise NotImplementedError("mode='constant' is not implemented yet")
185
- self._c_conv_mode = mp[self.mode]
186
-
187
- def _init_kernels(self):
188
- if self.kernel_ndim > 1:
189
- if np.abs(np.diff(self.kernel.shape)).max() > 0:
190
- raise NotImplementedError("Non-separable convolution with non-square kernels is not implemented yet")
191
- # Compile source module
192
- compile_options = [str("-DUSED_CONV_MODE=%d" % self._c_conv_mode)]
193
- fname = get_cuda_srcfile("convolution.cu")
194
- nabu_cuda_dir = dirname(fname)
195
- include_dirs = [nabu_cuda_dir]
196
- self.sourcemodule_kwargs["options"] = compile_options
197
- self.sourcemodule_kwargs["include_dirs"] = include_dirs
198
- with open(fname) as fid:
199
- cuda_src = fid.read()
200
- self._module = SourceModule(cuda_src, **self.sourcemodule_kwargs)
201
- # Blocks, grid
202
- self._block_size = {1: (32, 1, 1), 2: (32, 32, 1), 3: (16, 8, 8)}[self.data_ndim] # TODO tune
203
- self._n_blocks = tuple([int(updiv(a, b)) for a, b in zip(self.shape[::-1], self._block_size)])
204
- # Prepare cuda kernel calls
205
- self._cudakernel_signature = {
206
- 1: "PPPiiii",
207
- 2: "PPPiiiii",
208
- 3: "PPPiiiiii",
209
- }[self.kernel_ndim]
210
- self.cuda_kernels = {}
211
- for axis, kern_name in enumerate(self.use_case_kernels):
212
- self.cuda_kernels[axis] = self._module.get_function(kern_name)
213
- self.cuda_kernels[axis].prepare(self._cudakernel_signature)
214
-
215
- # Cuda kernel arguments
216
- kernel_args = [
217
- self._n_blocks,
218
- self._block_size,
219
- None,
220
- None,
221
- self.d_kernel.gpudata,
222
- np.int32(self.kernel.shape[0]),
223
- self.Nx,
224
- self.Ny,
225
- self.Nz,
226
- ]
227
- if self.kernel_ndim == 2:
228
- kernel_args.insert(5, np.int32(self.kernel.shape[1]))
229
- if self.kernel_ndim == 3:
230
- kernel_args.insert(5, np.int32(self.kernel.shape[2]))
231
- kernel_args.insert(6, np.int32(self.kernel.shape[1]))
232
- self.kernel_args = tuple(kernel_args)
233
- # If self.data_tmp is allocated, separable transforms can be performed
234
- # by a series of batched transforms, without any copy, by swapping refs.
235
- self.swap_pattern = None
236
- if self.separable:
237
- if self.data_tmp is not None:
238
- self.swap_pattern = {
239
- 2: [("data_in", "data_tmp"), ("data_tmp", "data_out")],
240
- 3: [
241
- ("data_in", "data_out"),
242
- ("data_out", "data_tmp"),
243
- ("data_tmp", "data_out"),
244
- ],
245
- }
246
- else:
247
- raise NotImplementedError("For now, data_tmp has to be allocated")
248
-
249
- def _get_swapped_arrays(self, i):
250
- """
251
- Get the input and output arrays to use when using a "swap pattern".
252
- Swapping refs enables to avoid copies between temp. array and output.
253
- For example, a separable 2D->1D convolution on 2D data reads:
254
- data_tmp = convol(data_input, kernel, axis=1) # step i=0
255
- data_out = convol(data_tmp, kernel, axis=0) # step i=1
256
-
257
- :param i: current step number of the separable convolution
258
- """
259
- n_batchs = len(self.axes)
260
- in_ref, out_ref = self.swap_pattern[n_batchs][i]
261
- d_in = getattr(self, in_ref)
262
- d_out = getattr(self, out_ref)
263
- return d_in, d_out
264
-
265
- def _configure_kernel_args(self, cuda_kernel_args, input_ref, output_ref):
266
- # TODO more elegant
267
- if isinstance(input_ref, self.cuda.array_class):
268
- input_ref = input_ref.gpudata
269
- if isinstance(output_ref, self.cuda.array_class):
270
- output_ref = output_ref.gpudata
271
- if input_ref is not None or output_ref is not None:
272
- cuda_kernel_args = list(cuda_kernel_args)
273
- if input_ref is not None:
274
- cuda_kernel_args[2] = input_ref
275
- if output_ref is not None:
276
- cuda_kernel_args[3] = output_ref
277
- cuda_kernel_args = tuple(cuda_kernel_args)
278
- return cuda_kernel_args
279
-
280
- @staticmethod
281
- def _check_dimensions(arr=None, shape=None, name="", dim_min=1, dim_max=3):
282
- if shape is not None:
283
- ndim = len(shape)
284
- elif arr is not None:
285
- ndim = arr.ndim
286
- else:
287
- raise ValueError("Please provide either arr= or shape=")
288
- if ndim < dim_min or ndim > dim_max:
289
- raise ValueError("%s dimensions should be between %d and %d" % (name, dim_min, dim_max))
290
- return ndim
291
-
292
- def _check_array(self, arr):
293
- if not (isinstance(arr, self.cuda.array_class) or isinstance(arr, np.ndarray)):
294
- raise TypeError("Expected either pycuda.gpuarray or numpy.ndarray")
295
- if arr.dtype != np.float32:
296
- raise TypeError("Data must be float32")
297
- if arr.shape != self.shape:
298
- raise ValueError("Expected data shape = %s" % str(self.shape))
299
-
300
- def _set_arrays(self, array, output=None):
301
- # Either copy H->D or update references.
302
- if isinstance(array, np.ndarray):
303
- self.data_in[:] = array[:]
304
- else:
305
- self._old_input_ref = self.data_in
306
- self.data_in = array
307
- data_in_ref = self.data_in
308
- if output is not None:
309
- if not (isinstance(output, np.ndarray)):
310
- self._old_output_ref = self.data_out
311
- self.data_out = output
312
- # Update Cuda kernel arguments with new array references
313
- self.kernel_args = self._configure_kernel_args(self.kernel_args, data_in_ref, self.data_out)
314
-
315
- def _separable_convolution(self):
316
- assert len(self.axes) == len(self.use_case_kernels)
317
- # Separable: one kernel call per data dimension
318
- for i, axis in enumerate(self.axes):
319
- in_ref, out_ref = self._get_swapped_arrays(i)
320
- self._batched_convolution(axis, input_ref=in_ref, output_ref=out_ref)
321
-
322
- def _batched_convolution(self, axis, input_ref=None, output_ref=None):
323
- # Batched: one kernel call in total
324
- cuda_kernel = self.cuda_kernels[axis]
325
- cuda_kernel_args = self._configure_kernel_args(self.kernel_args, input_ref, output_ref)
326
- ev = cuda_kernel.prepared_call(*cuda_kernel_args)
327
-
328
- def _nd_convolution(self):
329
- assert len(self.use_case_kernels) == 1
330
- cuda_kernel = self._module.get_function(self.use_case_kernels[0])
331
- ev = cuda_kernel.prepared_call(*self.kernel_args)
332
-
333
- def _recover_arrays_references(self):
334
- if self._old_input_ref is not None:
335
- self.data_in = self._old_input_ref
336
- self._old_input_ref = None
337
- if self._old_output_ref is not None:
338
- self.data_out = self._old_output_ref
339
- self._old_output_ref = None
340
- self.kernel_args = self._configure_kernel_args(self.kernel_args, self.data_in, self.data_out)
341
-
342
- def _get_output(self, output):
343
- if output is None:
344
- res = self.data_out.get()
345
- else:
346
- res = output
347
- if isinstance(output, np.ndarray):
348
- output[:] = self.data_out[:]
349
- self._recover_arrays_references()
350
- return res
351
-
352
- def convolve(self, array, output=None):
353
- """
354
- Convolve an array with the class kernel.
355
-
356
- :param array: Input array. Can be numpy.ndarray or pycuda.gpuarray.GPUArray.
357
- :param output: Output array. Can be numpy.ndarray or pycuda.gpuarray.GPUArray.
358
- """
359
- self._check_array(array)
360
- self._set_arrays(array, output=output)
361
- if self.axes is not None:
362
- if self.separable:
363
- self._separable_convolution()
364
- elif self.batched:
365
- assert len(self.axes) == 1
366
- self._batched_convolution(self.axes[0])
367
- # else: ND-ND convol
368
- else:
369
- # ND-ND convol
370
- self._nd_convolution()
371
-
372
- res = self._get_output(output)
373
- return res
374
-
375
- __call__ = convolve
@@ -1,163 +0,0 @@
1
- import numpy as np
2
- from ..utils import BaseClassError
3
-
4
-
5
- class _BaseFFT:
6
- """
7
- A base class for FFTs.
8
- """
9
-
10
- implem = "none"
11
- ProcessingCls = BaseClassError
12
-
13
- def __init__(self, shape, dtype, r2c=True, axes=None, normalize="rescale", **backend_options):
14
- """
15
- Base class for Fast Fourier Transform (FFT).
16
-
17
- Parameters
18
- ----------
19
- shape: list of int
20
- Shape of the input data
21
- dtype: str or numpy.dtype
22
- Data type of the input data
23
- r2c: bool, optional
24
- Whether to use real-to-complex transform for real-valued input. Default is True.
25
- axes: list of int, optional
26
- Axes along which FFT is computed.
27
- * For 2D transform: axes=(1,0)
28
- * For batched 1D transform of 2D image: axes=(-1,)
29
- normalize: str, optional
30
- Whether to normalize FFT and IFFT. Possible values are:
31
- * "rescale": in this case, Fourier data is divided by "N"
32
- before IFFT, so that IFFT(FFT(data)) = data.
33
- This corresponds to numpy norm=None i.e norm="backward".
34
- * "ortho": in this case, FFT and IFFT are adjoint of eachother,
35
- the transform is unitary. Both FFT and IFFT are scaled with 1/sqrt(N).
36
- * "none": no normalizatio is done : IFFT(FFT(data)) = data*N
37
-
38
- Other parameters
39
- -----------------
40
- backend_options: dict, optional
41
- Parameters to pass to CudaProcessing or OpenCLProcessing class.
42
- """
43
- self._init_backend(backend_options)
44
- self._set_dtypes(dtype, r2c)
45
- self._set_shape_and_axes(shape, axes)
46
- self._configure_batched_transform()
47
- self._configure_normalization(normalize)
48
- self._compute_fft_plans()
49
-
50
- def _init_backend(self, backend_options):
51
- self.processing = self.ProcessingCls(**backend_options)
52
-
53
- def _set_dtypes(self, dtype, r2c):
54
- self.dtype = np.dtype(dtype)
55
- dtypes_mapping = {
56
- np.dtype("float32"): np.complex64,
57
- np.dtype("float64"): np.complex128,
58
- np.dtype("complex64"): np.complex64,
59
- np.dtype("complex128"): np.complex128,
60
- }
61
- if self.dtype not in dtypes_mapping:
62
- raise ValueError("Invalid input data type: got %s" % self.dtype)
63
- self.dtype_out = dtypes_mapping[self.dtype]
64
- self.r2c = r2c
65
-
66
- def _set_shape_and_axes(self, shape, axes):
67
- # Input shape
68
- if np.isscalar(shape):
69
- shape = (shape,)
70
- self.shape = shape
71
- # Axes
72
- default_axes = tuple(range(len(self.shape)))
73
- if axes is None:
74
- self.axes = default_axes
75
- else:
76
- self.axes = tuple(np.array(default_axes)[np.array(axes)])
77
- # Output shape
78
- shape_out = self.shape
79
- if self.r2c:
80
- reduced_dim = self.axes[-1] if self.axes is not None else -1
81
- shape_out = list(shape_out)
82
- shape_out[reduced_dim] = shape_out[reduced_dim] // 2 + 1
83
- shape_out = tuple(shape_out)
84
- self.shape_out = shape_out
85
-
86
- def _configure_batched_transform(self):
87
- pass
88
-
89
- def _configure_normalization(self, normalize):
90
- pass
91
-
92
- def _compute_fft_plans(self):
93
- pass
94
-
95
-
96
- class _BaseVKFFT(_BaseFFT):
97
- """
98
- FFT using VKFFT backend
99
- """
100
-
101
- implem = "vkfft"
102
- backend = "none"
103
- ProcessingCls = BaseClassError
104
- vkffs_cls = BaseClassError
105
-
106
- def _configure_batched_transform(self):
107
- if self.axes is not None and len(self.shape) == len(self.axes):
108
- self.axes = None
109
- return
110
- if self.r2c:
111
- # batched Real-to-complex transforms are supported only along fast axes
112
- if not (is_fast_axes(len(self.shape), self.axes)):
113
- raise ValueError("For %dD R2C, only batched transforms along fast axes are allowed" % (len(self.shape)))
114
- self._vkfft_ndim = len(self.axes)
115
- self.axes = None # vkfft still can do a batched transform by providing dim=XX, axes=None
116
-
117
- def _configure_normalization(self, normalize):
118
- self.normalize = normalize
119
- self._vkfft_norm = {
120
- "rescale": 1,
121
- "backward": 1,
122
- "ortho": "ortho",
123
- "none": 0,
124
- }.get(self.normalize, 1)
125
-
126
- def _set_shape_and_axes(self, shape, axes):
127
- super()._set_shape_and_axes(shape, axes)
128
- self._vkfft_ndim = None
129
-
130
- def _compute_fft_plans(self):
131
- self._vkfft_plan = self.vkffs_cls(
132
- self.shape,
133
- self.dtype,
134
- ndim=self._vkfft_ndim,
135
- inplace=False,
136
- norm=self._vkfft_norm,
137
- r2c=self.r2c,
138
- dct=False,
139
- axes=self.axes,
140
- strides=None,
141
- **self._vkfft_other_init_kwargs,
142
- )
143
-
144
- def fft(self, array, output=None):
145
- if output is None:
146
- output = self.output_fft = self.processing.allocate_array(
147
- "output_fft", self.shape_out, dtype=self.dtype_out
148
- )
149
- return self._vkfft_plan.fft(array, dest=output)
150
-
151
- def ifft(self, array, output=None):
152
- if output is None:
153
- output = self.output_ifft = self.processing.allocate_array("output_ifft", self.shape, dtype=self.dtype)
154
- return self._vkfft_plan.ifft(array, dest=output)
155
-
156
-
157
- def is_fast_axes(ndim, axes):
158
- """
159
- Return true if "axes" are the fast dimensions
160
- """
161
- all_axes = list(range(ndim))
162
- axes = sorted([ax + ndim if ax < 0 else ax for ax in axes]) # transform "-1" to an actual axis index (1 for 2D)
163
- return all_axes[-len(axes) :] == axes