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
@@ -1,6 +0,0 @@
1
- from silx.utils.enum import Enum as _Enum
2
-
3
-
4
- class StitchingType(_Enum):
5
- Z_PREPROC = "z-preproc"
6
- Z_POSTPROC = "z-postproc"
@@ -1,155 +0,0 @@
1
- from copy import copy
2
- from dataclasses import dataclass
3
- import numpy
4
- from math import ceil
5
-
6
- from nabu.stitching.overlap import ZStichOverlapKernel
7
-
8
-
9
- @dataclass
10
- class _FrameCompositionBase:
11
- def compose(self, output_frame: numpy.ndarray, input_frames: tuple):
12
- raise NotImplementedError("Base class")
13
-
14
-
15
- @dataclass
16
- class ZFrameComposition(_FrameCompositionBase):
17
- """
18
- class used to define intervals to know where to dump raw data or stitched data according to requested policy.
19
- The idea is to create this once for all for one stitching operation and reuse it for each frame.
20
- """
21
-
22
- local_start_y: tuple
23
- local_end_y: tuple
24
- global_start_y: tuple
25
- global_end_y: tuple
26
-
27
- def browse(self):
28
- for i in range(len(self.local_start_y)):
29
- yield (
30
- self.local_start_y[i],
31
- self.local_end_y[i],
32
- self.global_start_y[i],
33
- self.global_end_y[i],
34
- )
35
-
36
- def compose(self, output_frame: numpy.ndarray, input_frames: tuple):
37
- if not output_frame.ndim in (2, 3):
38
- raise TypeError(
39
- f"output_frame is expected to be 2D (gray scale) or 3D (RGB(A)) and not {output_frame.ndim}"
40
- )
41
- for (
42
- global_start_y,
43
- global_end_y,
44
- local_start_y,
45
- local_end_y,
46
- input_frame,
47
- ) in zip(
48
- self.global_start_y,
49
- self.global_end_y,
50
- self.local_start_y,
51
- self.local_end_y,
52
- input_frames,
53
- ):
54
- if input_frame is not None:
55
- output_frame[global_start_y:global_end_y] = input_frame[local_start_y:local_end_y]
56
-
57
- @staticmethod
58
- def compute_raw_frame_compositions(frames: tuple, key_lines: tuple, overlap_kernels: tuple, stitching_axis):
59
- """
60
- compute frame composition for raw data
61
-
62
- warning: we expect frames to be ordered y downward and the frame order to keep this ordering
63
- """
64
- assert len(frames) == len(overlap_kernels) + 1 == len(key_lines) + 1
65
-
66
- global_start_ys = [0]
67
-
68
- # extend shifts and kernels to have a first shift of 0 and two overlaps values at 0 to
69
- # generalize processing
70
- local_start_ys = [0]
71
-
72
- local_start_ys.extend(
73
- [ceil(key_line[1] + kernel.overlap_size / 2) for (key_line, kernel) in zip(key_lines, overlap_kernels)]
74
- )
75
- local_end_ys = list(
76
- [ceil(key_line[0] - kernel.overlap_size / 2) for (key_line, kernel) in zip(key_lines, overlap_kernels)]
77
- )
78
- local_end_ys.append(frames[-1].shape[stitching_axis])
79
-
80
- for (
81
- new_local_start_y,
82
- new_local_end_y,
83
- kernel,
84
- ) in zip(local_start_ys, local_end_ys, overlap_kernels):
85
- global_start_ys.append(global_start_ys[-1] + (new_local_end_y - new_local_start_y) + kernel.overlap_size)
86
-
87
- # global end can be easily found from global start + local start and end
88
- global_end_ys = []
89
- for global_start_y, new_local_start_y, new_local_end_y in zip(global_start_ys, local_start_ys, local_end_ys):
90
- global_end_ys.append(global_start_y + new_local_end_y - new_local_start_y)
91
-
92
- return ZFrameComposition(
93
- local_start_y=tuple(local_start_ys),
94
- local_end_y=tuple(local_end_ys),
95
- global_start_y=tuple(global_start_ys),
96
- global_end_y=tuple(global_end_ys),
97
- )
98
-
99
- @staticmethod
100
- def compute_stitch_frame_composition(frames, key_lines: tuple, overlap_kernels: tuple, stitching_axis: int):
101
- """
102
- compute frame composition for stiching.
103
- """
104
- assert len(frames) == len(overlap_kernels) + 1 == len(key_lines) + 1
105
- assert stitching_axis in (0, 1, 2)
106
-
107
- # position in the stitched frame;
108
- local_start_ys = [0] * len(overlap_kernels)
109
- local_end_ys = [kernel.overlap_size for kernel in overlap_kernels]
110
-
111
- # position in the global frame. For this one it is simpler to rely on the raw frame composition
112
- composition_raw = ZFrameComposition.compute_raw_frame_compositions(
113
- frames=frames,
114
- key_lines=key_lines,
115
- overlap_kernels=overlap_kernels,
116
- stitching_axis=stitching_axis,
117
- )
118
- global_start_ys = composition_raw.global_end_y[:-1]
119
- global_end_ys = composition_raw.global_start_y[1:]
120
-
121
- return ZFrameComposition(
122
- local_start_y=tuple(local_start_ys),
123
- local_end_y=tuple(local_end_ys),
124
- global_start_y=tuple(global_start_ys),
125
- global_end_y=tuple(global_end_ys),
126
- )
127
-
128
- @staticmethod
129
- def pprint_z_stitching(raw_composition, stitch_composition):
130
- """
131
- util to display what the output of the z stitch will looks like from composition
132
- """
133
- for i_frame, (raw_comp, stitch_comp) in enumerate(zip(raw_composition.browse(), stitch_composition.browse())):
134
- raw_local_start, raw_local_end, raw_global_start, raw_global_end = raw_comp
135
-
136
- print(
137
- f"stitch_frame[{raw_global_start}:{raw_global_end}] = frame_{i_frame}[{raw_local_start}:{raw_local_end}]"
138
- )
139
-
140
- (
141
- stitch_local_start,
142
- stitch_local_end,
143
- stitch_global_start,
144
- stitch_global_end,
145
- ) = stitch_comp
146
-
147
- print(
148
- f"stitch_frame[{stitch_global_start}:{stitch_global_end}] = stitched_frame_{i_frame}[{stitch_local_start}:{stitch_local_end}]"
149
- )
150
- else:
151
- i_frame += 1
152
- raw_local_start, raw_local_end, raw_global_start, raw_global_end = list(raw_composition.browse())[-1]
153
- print(
154
- f"stitch_frame[{raw_global_start}:{raw_global_end}] = frame_{i_frame}[{raw_local_start}:{raw_local_end}]"
155
- )
@@ -1,373 +0,0 @@
1
- # coding: utf-8
2
- # /*##########################################################################
3
- #
4
- # Copyright (c) 2016-2017 European Synchrotron Radiation Facility
5
- #
6
- # Permission is hereby granted, free of charge, to any person obtaining a copy
7
- # of this software and associated documentation files (the "Software"), to deal
8
- # in the Software without restriction, including without limitation the rights
9
- # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
10
- # copies of the Software, and to permit persons to whom the Software is
11
- # furnished to do so, subject to the following conditions:
12
- #
13
- # The above copyright notice and this permission notice shall be included in
14
- # all copies or substantial portions of the Software.
15
- #
16
- # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
17
- # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
18
- # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
19
- # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
20
- # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
21
- # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
22
- # THE SOFTWARE.
23
- #
24
- # ###########################################################################*/
25
-
26
- __authors__ = ["H. Payno"]
27
- __license__ = "MIT"
28
- __date__ = "10/05/2022"
29
-
30
-
31
- import numpy
32
- import logging
33
- from typing import Optional, Union
34
- from silx.utils.enum import Enum as _Enum
35
- from nabu.misc import fourier_filters
36
- from scipy.fft import rfftn as local_fftn
37
- from scipy.fft import irfftn as local_ifftn
38
- from tomoscan.utils.geometry import BoundingBox1D
39
-
40
- _logger = logging.getLogger(__name__)
41
-
42
-
43
- class OverlapStitchingStrategy(_Enum):
44
- MEAN = "mean"
45
- COSINUS_WEIGHTS = "cosinus weights"
46
- LINEAR_WEIGHTS = "linear weights"
47
- CLOSEST = "closest"
48
- IMAGE_MINIMUM_DIVERGENCE = "image minimum divergence"
49
- HIGHER_SIGNAL = "higher signal"
50
-
51
-
52
- DEFAULT_OVERLAP_STRATEGY = OverlapStitchingStrategy.COSINUS_WEIGHTS
53
-
54
- DEFAULT_OVERLAP_SIZE = None # could also be an int
55
- # default overlap to be take for stitching. Ig None: take the largest possible area
56
-
57
-
58
- class OverlapKernelBase:
59
- pass
60
-
61
-
62
- class ZStichOverlapKernel(OverlapKernelBase):
63
- """
64
- class used to define overlap between two scans and create stitch between frames (`stitch` function)
65
- """
66
-
67
- DEFAULT_HIGH_FREQUENCY_THRESHOLD = 2
68
-
69
- def __init__(
70
- self,
71
- frame_width: int,
72
- stitching_strategy: OverlapStitchingStrategy = DEFAULT_OVERLAP_STRATEGY,
73
- overlap_size: int = DEFAULT_OVERLAP_SIZE,
74
- extra_params: Optional[dict] = None,
75
- ) -> None:
76
- """ """
77
- from nabu.stitching.config import KEY_THRESHOLD_FREQUENCY # avoid acylic import
78
-
79
- if not isinstance(overlap_size, int) and overlap_size > 0:
80
- raise TypeError(
81
- f"overlap_size is expected to be a positive int, {overlap_size} - not {overlap_size} ({type(overlap_size)})"
82
- )
83
- if not isinstance(frame_width, int) or not frame_width > 0:
84
- raise TypeError(
85
- f"frame_width is expected to be a positive int, {frame_width} - not {frame_width} ({type(frame_width)})"
86
- )
87
-
88
- self._overlap_size = abs(overlap_size)
89
- self._frame_width = frame_width
90
- self._stitching_strategy = OverlapStitchingStrategy.from_value(stitching_strategy)
91
- self._weights_img_1 = None
92
- self._weights_img_2 = None
93
- if extra_params is None:
94
- extra_params = {}
95
- self._high_frequency_threshold = extra_params.get(
96
- KEY_THRESHOLD_FREQUENCY, self.DEFAULT_HIGH_FREQUENCY_THRESHOLD
97
- )
98
-
99
- def __str__(self) -> str:
100
- return f"z-stitching kernel (policy={self.stitching_strategy.value}, overlap_size={self.overlap_size}, frame={self._frame_width})"
101
-
102
- @staticmethod
103
- def __check_img(img, name):
104
- if not isinstance(img, numpy.ndarray) and img.ndim == 2:
105
- raise ValueError(f"{name} is expected to be 2D numpy array")
106
-
107
- @property
108
- def overlap_size(self) -> int:
109
- return self._overlap_size
110
-
111
- @overlap_size.setter
112
- def overlap_size(self, size: int):
113
- if not isinstance(size, int):
114
- raise TypeError(f"height expects a int ({type(size)} provided instead)")
115
- if not size >= 0:
116
- raise ValueError(f"height is expected to be positive")
117
- self._overlap_size = abs(size)
118
- # update weights if needed
119
- if self._weights_img_1 is not None or self._weights_img_2 is not None:
120
- self.compute_weights()
121
-
122
- @property
123
- def img_2(self) -> numpy.ndarray:
124
- return self._img_2
125
-
126
- @property
127
- def weights_img_1(self) -> Optional[numpy.ndarray]:
128
- return self._weights_img_1
129
-
130
- @property
131
- def weights_img_2(self) -> Optional[numpy.ndarray]:
132
- return self._weights_img_2
133
-
134
- @property
135
- def stitching_strategy(self) -> OverlapStitchingStrategy:
136
- return self._stitching_strategy
137
-
138
- def compute_weights(self):
139
- if self.stitching_strategy is OverlapStitchingStrategy.MEAN:
140
- weights_img_1 = numpy.ones(self._overlap_size) * 0.5
141
- weights_img_2 = weights_img_1[::-1]
142
- elif self.stitching_strategy is OverlapStitchingStrategy.CLOSEST:
143
- n_item = self._overlap_size // 2 + self._overlap_size % 2
144
- weights_img_1 = numpy.concatenate(
145
- [
146
- numpy.ones(n_item),
147
- numpy.zeros(self._overlap_size - n_item),
148
- ]
149
- )
150
- weights_img_2 = numpy.concatenate(
151
- [
152
- numpy.zeros(n_item),
153
- numpy.ones(self._overlap_size - n_item),
154
- ]
155
- )
156
- elif self.stitching_strategy is OverlapStitchingStrategy.LINEAR_WEIGHTS:
157
- weights_img_1 = numpy.linspace(1.0, 0.0, self._overlap_size)
158
- weights_img_2 = weights_img_1[::-1]
159
- elif self.stitching_strategy is OverlapStitchingStrategy.COSINUS_WEIGHTS:
160
- angles = numpy.linspace(0.0, numpy.pi / 2.0, self._overlap_size)
161
- weights_img_1 = numpy.cos(angles) ** 2
162
- weights_img_2 = numpy.sin(angles) ** 2
163
- elif self.stitching_strategy in (
164
- OverlapStitchingStrategy.IMAGE_MINIMUM_DIVERGENCE,
165
- OverlapStitchingStrategy.HIGHER_SIGNAL,
166
- ):
167
- # those strategies are not using constant weights but have treatments depending on the provided img_1 and mg_2 during stitching
168
- return
169
- else:
170
- raise NotImplementedError(f"{self.stitching_strategy} not implemented")
171
-
172
- self._weights_img_1 = weights_img_1.reshape(-1, 1) * numpy.ones(self._frame_width).reshape(1, -1)
173
- self._weights_img_2 = weights_img_2.reshape(-1, 1) * numpy.ones(self._frame_width).reshape(1, -1)
174
-
175
- def stitch(self, img_1, img_2, check_input=True) -> tuple:
176
- """Compute overlap region from the defined strategy"""
177
- if check_input:
178
- self.__check_img(img_1, "img_1")
179
- self.__check_img(img_2, "img_2")
180
-
181
- if img_1.shape != img_2.shape:
182
- raise ValueError(
183
- f"both images are expected to be of the same shape to apply stitch ({img_1.shape} vs {img_2.shape})"
184
- )
185
-
186
- if self._stitching_strategy is OverlapStitchingStrategy.IMAGE_MINIMUM_DIVERGENCE:
187
- return (
188
- compute_image_minimum_divergence(
189
- img_1=img_1, img_2=img_2, high_frequency_threshold=self._high_frequency_threshold
190
- ),
191
- None,
192
- None,
193
- )
194
- elif self._stitching_strategy is OverlapStitchingStrategy.HIGHER_SIGNAL:
195
- return (
196
- compute_image_higher_signal(img_1=img_1, img_2=img_2),
197
- None,
198
- None,
199
- )
200
- else:
201
- if self.weights_img_1 is None or self.weights_img_2 is None:
202
- self.compute_weights()
203
-
204
- return (
205
- img_1 * self.weights_img_1 + img_2 * self.weights_img_2,
206
- self.weights_img_1,
207
- self.weights_img_2,
208
- )
209
-
210
-
211
- def compute_image_minimum_divergence(img_1: numpy.ndarray, img_2: numpy.ndarray, high_frequency_threshold):
212
- """
213
- Algorithm to improve treatment of high frequency.
214
-
215
- It split the two images into two parts: high frequency and low frequency.
216
-
217
- The two low frequency part will be stitched using a 'sinusoidal' / cosinus weights approach.
218
- When the two high frequency parts will be stitched by taking the lower divergent pixels
219
- """
220
-
221
- # split low and high frequencies
222
- def split_image(image: numpy.ndarray, threshold: int) -> tuple:
223
- """split an image to return (low_frequency, high_frequency)"""
224
-
225
- lowpass_filter = fourier_filters.get_lowpass_filter(
226
- image.shape[-2:],
227
- cutoff_par=threshold,
228
- use_rfft=True,
229
- data_type=image.dtype,
230
- )
231
- highpass_filter = fourier_filters.get_highpass_filter(
232
- image.shape[-2:],
233
- cutoff_par=threshold,
234
- use_rfft=True,
235
- data_type=image.dtype,
236
- )
237
- low_fre_part = local_ifftn(local_fftn(image, axes=(-2, -1)) * lowpass_filter, axes=(-2, -1)).real
238
- high_fre_part = local_ifftn(local_fftn(image, axes=(-2, -1)) * highpass_filter, axes=(-2, -1)).real
239
- return (low_fre_part, high_fre_part)
240
-
241
- low_freq_img_1, high_freq_img_1 = split_image(img_1, threshold=high_frequency_threshold)
242
- low_freq_img_2, high_freq_img_2 = split_image(img_2, threshold=high_frequency_threshold)
243
-
244
- # handle low frequency
245
- low_freq_stitching_kernel = ZStichOverlapKernel(
246
- frame_width=img_1.shape[1],
247
- stitching_strategy=OverlapStitchingStrategy.COSINUS_WEIGHTS,
248
- overlap_size=img_1.shape[0],
249
- )
250
- low_freq_stitched = low_freq_stitching_kernel.stitch(
251
- img_1=low_freq_img_1,
252
- img_2=low_freq_img_2,
253
- check_input=False,
254
- )[0]
255
-
256
- # handle high frequency
257
- mean_high_frequency = numpy.mean([high_freq_img_1, high_freq_img_2])
258
- assert numpy.isscalar(mean_high_frequency)
259
- high_freq_distance_img_1 = numpy.abs(high_freq_img_1 - mean_high_frequency)
260
- high_freq_distance_img_2 = numpy.abs(high_freq_img_2 - mean_high_frequency)
261
- high_freq_stitched = numpy.where(
262
- high_freq_distance_img_1 >= high_freq_distance_img_2, high_freq_distance_img_2, high_freq_distance_img_1
263
- )
264
-
265
- # merge back low and high frequencies together
266
- def merge_images(low_freq: numpy.ndarray, high_freq: numpy.ndarray) -> numpy.ndarray:
267
- """merge two part of an image. The low frequency part with the high frequency part"""
268
- return low_freq + high_freq
269
-
270
- return merge_images(low_freq_stitched, high_freq_stitched)
271
-
272
-
273
- def compute_image_higher_signal(img_1: numpy.ndarray, img_2: numpy.ndarray):
274
- """
275
- the higher signal will pick pixel on the image having the higher signal.
276
- A use case is that if there is some artefacts on images which creates stripes (from scintillator artefacts for example)
277
- it could be removed from this method
278
- """
279
- # note: to be think about. But maybe it can be interesting to rescale img_1 and img_2
280
- # to ge something more coherent
281
- return numpy.where(img_1 >= img_2, img_1, img_2)
282
-
283
-
284
- def check_overlaps(frames: Union[tuple, numpy.ndarray], positions: tuple, axis: int, raise_error: bool):
285
- """
286
- check over frames if there is a single overlap other juxtaposed frames (at most and at least)
287
-
288
- :param frames: liste of ordered / sorted frames along axis to test (from higher to lower)
289
- :param positions: positions of frames in 3D space as (position axis 0, position axis 1, position axis 2)
290
- :param axis: axis to check
291
- :param raise_error: if True then raise an error if two frames don't have at least and at most one overlap. Else log an error
292
- """
293
- if not isinstance(frames, (tuple, numpy.ndarray)):
294
- raise TypeError(f"frames is expected to be a tuple or a numpy array. Get {type(frames)} instead")
295
- if not isinstance(positions, tuple):
296
- raise TypeError(f"positions is expected to be a tuple. Get {type(positions)} instead")
297
- assert isinstance(axis, int), "axis is expected to be an int"
298
- assert isinstance(raise_error, bool), "raise_error is expected to be a bool"
299
-
300
- def treat_error(error_msg: str):
301
- if raise_error:
302
- raise ValueError(error_msg)
303
- else:
304
- _logger.error(raise_error)
305
-
306
- # convert each frame to appropriate bounding box according to the axis
307
- def convert_to_bb(frame: numpy.ndarray, position: tuple, axis: int):
308
- assert isinstance(axis, int)
309
- assert isinstance(position, tuple), f"position expected a tuple. Get {type(position)} instead"
310
- start_frame = position[axis] - frame.shape[axis] // 2
311
- end_frame = start_frame + frame.shape[axis]
312
- return BoundingBox1D(start_frame, end_frame)
313
-
314
- bounding_boxes = {
315
- convert_to_bb(frame=frame, position=position, axis=axis): position for frame, position in zip(frames, positions)
316
- }
317
-
318
- def get_frame_index(my_bb) -> str:
319
- bb_index = tuple(bounding_boxes.keys()).index(my_bb) + 1
320
- if bb_index in (1, 21, 31):
321
- return f"{bb_index}st"
322
- elif bb_index in (2, 22, 32):
323
- return f"{bb_index}nd"
324
- elif bb_index == (3, 23, 33):
325
- return f"{bb_index}rd"
326
- else:
327
- return f"{bb_index}th"
328
-
329
- # check that theres an overlap between two juxtaposed bb (or frame at the end)
330
- all_bounding_boxes = tuple(bounding_boxes.keys())
331
- bb_with_expected_overlap = [
332
- (bb_frame, bb_next_frame) for bb_frame, bb_next_frame in zip(all_bounding_boxes[:-1], all_bounding_boxes[1:])
333
- ]
334
-
335
- for bb_pair in bb_with_expected_overlap:
336
- bb_frame, bb_next_frame = bb_pair
337
- if bb_frame.max < bb_next_frame.min:
338
- treat_error(f"provided frames seems un sorted (from the higher to the lower)")
339
- if bb_frame.min < bb_next_frame.min:
340
- treat_error(
341
- f"Seems like {get_frame_index(bb_frame)} frame is fully overlaping with frame {get_frame_index(bb_next_frame)}"
342
- )
343
- if bb_frame.get_overlap(bb_next_frame) is None:
344
- treat_error(
345
- f"no overlap found between two juxtaposed frames - {get_frame_index(bb_frame)} and {get_frame_index(bb_next_frame)}"
346
- )
347
-
348
- # check there is no overlap between none juxtaposed bb
349
- def pick_all_none_juxtaposed_bb(index, my_bounding_boxes: tuple):
350
- """return all the bounding boxes to check for the index 'index':
351
-
352
- :return: (tested_bounding_box, bounding_boxes_to_test)
353
- """
354
- my_bounding_boxes = {bb_index: bb for bb_index, bb in enumerate(my_bounding_boxes)}
355
- bounding_boxes = dict(
356
- filter(
357
- lambda pair: pair[0] not in (index - 1, index, index + 1),
358
- my_bounding_boxes.items(),
359
- )
360
- )
361
- return my_bounding_boxes[index], bounding_boxes.values()
362
-
363
- bb_without_expected_overlap = [
364
- pick_all_none_juxtaposed_bb(index, all_bounding_boxes) for index in range(len(all_bounding_boxes))
365
- ]
366
-
367
- for bb_pair in bb_without_expected_overlap:
368
- bb_frame, bb_not_juxtaposed_frames = bb_pair
369
- for bb_not_juxtaposed_frame in bb_not_juxtaposed_frames:
370
- if bb_frame.get_overlap(bb_not_juxtaposed_frame) is not None:
371
- treat_error(
372
- f"overlap found between two frames not juxtaposed - {bounding_boxes[bb_frame]} and {bounding_boxes[bb_not_juxtaposed_frame]}"
373
- )
@@ -1,60 +0,0 @@
1
- import numpy
2
- from silx.utils.enum import Enum as _Enum
3
-
4
-
5
- class SampleSide(_Enum):
6
- LEFT = "left"
7
- RIGHT = "right"
8
-
9
-
10
- class Method(_Enum):
11
- MEAN = "mean"
12
- MEDIAN = "median"
13
-
14
-
15
- def normalize_frame(
16
- frame: numpy.ndarray, side: SampleSide, method: Method, sample_width: int = 50, margin_before_sample: int = 0
17
- ):
18
- """
19
- normalize the frame from a sample section picked at the left of the right of the frame
20
-
21
- :param frame: frame to normalize
22
- :param SampleSide side: side to pick the sample
23
- :param Method method: normalization method
24
- :param int sample_width: sample width
25
- :param int margin: margin before the sampling area
26
- """
27
- if not isinstance(frame, numpy.ndarray):
28
- raise TypeError(f"Frame is expected to be a 2D numpy array.")
29
- if frame.ndim != 2:
30
- raise TypeError(f"Frame is expected to be a 2D numpy array. Get {frame.ndim}D")
31
- side = SampleSide.from_value(side)
32
- method = Method.from_value(method)
33
-
34
- if frame.shape[1] < sample_width + margin_before_sample:
35
- raise ValueError(
36
- f"frame width ({frame.shape[1]}) < sample_width + margin ({sample_width + margin_before_sample})"
37
- )
38
-
39
- # create sample
40
- if side is SampleSide.LEFT:
41
- sample_start = margin_before_sample
42
- sample_end = margin_before_sample + sample_width
43
- sample = frame[:, sample_start:sample_end]
44
- elif side is SampleSide.RIGHT:
45
- sample_start = frame.shape[1] - (sample_width + margin_before_sample)
46
- sample_end = frame.shape[1] - margin_before_sample
47
- sample = frame[:, sample_start:sample_end]
48
- else:
49
- raise ValueError(f"side {side.value} not handled")
50
-
51
- # do normalization
52
- if method is Method.MEAN:
53
- normalization_array = numpy.mean(sample, axis=1)
54
- elif method is Method.MEDIAN:
55
- normalization_array = numpy.median(sample, axis=1)
56
- else:
57
- raise ValueError(f"side {side.value} not handled")
58
- for line in range(normalization_array.shape[0]):
59
- frame[line, :] -= normalization_array[line]
60
- return frame