nabu 2024.1.0rc4__py3-none-any.whl → 2024.1.1__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 (2092) hide show
  1. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/doc/conf.py +137 -0
  2. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/doc/create_conf_doc.py +38 -0
  3. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/doc/get_mathjax.py +34 -0
  4. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/__init__.py +17 -0
  5. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/bootstrap.py +88 -0
  6. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/bootstrap_stitching.py +69 -0
  7. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/cast_volume.py +272 -0
  8. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/cli_configs.py +626 -0
  9. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/compare_volumes.py +94 -0
  10. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/composite_cor.py +144 -0
  11. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/correct_rot.py +70 -0
  12. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/create_distortion_map_from_poly.py +153 -0
  13. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/diag_to_pix.py +358 -0
  14. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/diag_to_rot.py +449 -0
  15. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/double_flatfield.py +143 -0
  16. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/generate_header.py +261 -0
  17. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/histogram.py +197 -0
  18. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/multicor.py +90 -0
  19. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/nx_z_splitter.py +125 -0
  20. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/parse_reconstruction_log.py +151 -0
  21. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/prepare_weights_double.py +163 -0
  22. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/reconstruct.py +120 -0
  23. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/reconstruct_helical.py +116 -0
  24. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/reduce_dark_flat.py +181 -0
  25. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/rotate.py +162 -0
  26. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/shrink_dataset.py +98 -0
  27. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/stitching.py +85 -0
  28. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/tests/test_reduce_dark_flat.py +78 -0
  29. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/utils.py +33 -0
  30. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/validator.py +110 -0
  31. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/__init__.py +0 -0
  32. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/convolution.py +8 -0
  33. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/fft.py +4 -0
  34. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/kernel.py +97 -0
  35. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/medfilt.py +6 -0
  36. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/padding.py +6 -0
  37. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/processing.py +75 -0
  38. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/tests/__init__.py +1 -0
  39. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/utils.py +331 -0
  40. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/__init__.py +12 -0
  41. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/alignment.py +578 -0
  42. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/cor.py +1621 -0
  43. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/cor_sino.py +183 -0
  44. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/distortion.py +112 -0
  45. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/focus.py +362 -0
  46. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/__init__.py +0 -0
  47. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_alignment.py +70 -0
  48. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_cor.py +472 -0
  49. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_focus.py +105 -0
  50. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_tilt.py +41 -0
  51. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_translation.py +78 -0
  52. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tilt.py +214 -0
  53. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/translation.py +193 -0
  54. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/utils.py +39 -0
  55. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/__init__.py +2 -0
  56. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/cast_volume.py +371 -0
  57. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/detector_distortion.py +305 -0
  58. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/reader.py +628 -0
  59. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/reader_helical.py +114 -0
  60. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tests/__init__.py +0 -0
  61. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tests/test_cast_volume.py +339 -0
  62. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tests/test_detector_distortion.py +178 -0
  63. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tests/test_writers.py +187 -0
  64. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tiffwriter_zmm.py +99 -0
  65. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/utils.py +263 -0
  66. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/writer.py +892 -0
  67. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/__init__.py +0 -0
  68. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/binning.py +98 -0
  69. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/fftshift.py +6 -0
  70. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/filters.py +24 -0
  71. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/fourier_filters.py +152 -0
  72. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/histogram.py +6 -0
  73. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/histogram_cuda.py +8 -0
  74. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/kernel_base.py +4 -0
  75. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/padding.py +83 -0
  76. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/padding_base.py +6 -0
  77. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/processing_base.py +4 -0
  78. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/rotation.py +6 -0
  79. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/rotation_cuda.py +6 -0
  80. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/tests/__init__.py +1 -0
  81. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/tests/test_binning.py +48 -0
  82. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/tests/test_interpolation.py +70 -0
  83. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/transpose.py +6 -0
  84. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/unsharp.py +4 -0
  85. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/unsharp_cuda.py +6 -0
  86. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/unsharp_opencl.py +8 -0
  87. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/utils.py +117 -0
  88. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/__init__.py +0 -0
  89. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/fft.py +6 -0
  90. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/kernel.py +135 -0
  91. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/memcpy.py +35 -0
  92. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/padding.py +6 -0
  93. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/processing.py +62 -0
  94. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/tests/__init__.py +0 -0
  95. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/utils.py +292 -0
  96. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/__init__.py +0 -0
  97. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/config.py +265 -0
  98. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/config_validators.py +589 -0
  99. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/datadump.py +164 -0
  100. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/dataset_validator.py +211 -0
  101. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/detector_distortion_provider.py +20 -0
  102. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/estimators.py +1012 -0
  103. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fallback_utils.py +149 -0
  104. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/__init__.py +0 -0
  105. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/chunked.py +849 -0
  106. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/chunked_cuda.py +152 -0
  107. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/computations.py +260 -0
  108. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/dataset_validator.py +63 -0
  109. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/nabu_config.py +590 -0
  110. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/processconfig.py +825 -0
  111. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/reconstruction.py +851 -0
  112. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/__init__.py +0 -0
  113. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/dataset_validator.py +19 -0
  114. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/fbp.py +147 -0
  115. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/filtering.py +246 -0
  116. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/gridded_accumulator.py +575 -0
  117. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_chunked_regridded.py +1670 -0
  118. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_chunked_regridded_cuda.py +119 -0
  119. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_reconstruction.py +598 -0
  120. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_utils.py +42 -0
  121. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/nabu_config.py +175 -0
  122. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/processconfig.py +62 -0
  123. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/span_strategy.py +483 -0
  124. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/__init__.py +0 -0
  125. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/test_accumulator.py +157 -0
  126. 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 +355 -0
  127. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/test_strategy.py +61 -0
  128. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/utils.py +51 -0
  129. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/weight_balancer.py +101 -0
  130. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/params.py +163 -0
  131. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/processconfig.py +210 -0
  132. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/tests/test_chunk_reader.py +78 -0
  133. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/tests/test_estimators.py +149 -0
  134. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/utils.py +116 -0
  135. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/writer.py +193 -0
  136. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/xrdct/__init__.py +0 -0
  137. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/__init__.py +7 -0
  138. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/alignment.py +11 -0
  139. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ccd.py +161 -0
  140. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ccd_cuda.py +169 -0
  141. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ctf.py +361 -0
  142. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ctf_cuda.py +142 -0
  143. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/distortion.py +92 -0
  144. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/double_flatfield.py +212 -0
  145. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/double_flatfield_cuda.py +174 -0
  146. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/double_flatfield_variable_region.py +68 -0
  147. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/flatfield.py +448 -0
  148. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/flatfield_cuda.py +144 -0
  149. build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/flatfield_variable_region.py +79 -0
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  1981. build/lib/nabu/processing/__init__.py +0 -0
  1982. build/lib/nabu/processing/convolution_cuda.py +375 -0
  1983. build/lib/nabu/processing/fft_base.py +163 -0
  1984. build/lib/nabu/processing/fft_cuda.py +256 -0
  1985. build/lib/nabu/processing/fft_opencl.py +54 -0
  1986. build/lib/nabu/processing/fftshift.py +134 -0
  1987. build/lib/nabu/processing/histogram.py +286 -0
  1988. build/lib/nabu/processing/histogram_cuda.py +103 -0
  1989. build/lib/nabu/processing/kernel_base.py +126 -0
  1990. build/lib/nabu/processing/medfilt_cuda.py +159 -0
  1991. build/lib/nabu/processing/muladd.py +29 -0
  1992. build/lib/nabu/processing/muladd_cuda.py +68 -0
  1993. build/lib/nabu/processing/padding_base.py +71 -0
  1994. build/lib/nabu/processing/padding_cuda.py +75 -0
  1995. build/lib/nabu/processing/padding_opencl.py +77 -0
  1996. build/lib/nabu/processing/processing_base.py +123 -0
  1997. build/lib/nabu/processing/roll_opencl.py +64 -0
  1998. build/lib/nabu/processing/rotation.py +63 -0
  1999. build/lib/nabu/processing/rotation_cuda.py +66 -0
  2000. build/lib/nabu/processing/tests/__init__.py +0 -0
  2001. build/lib/nabu/processing/tests/test_fft.py +268 -0
  2002. build/lib/nabu/processing/tests/test_fftshift.py +71 -0
  2003. build/lib/nabu/processing/tests/test_histogram.py +55 -0
  2004. build/lib/nabu/processing/tests/test_medfilt.py +77 -0
  2005. build/lib/nabu/processing/tests/test_muladd.py +54 -0
  2006. build/lib/nabu/processing/tests/test_padding.py +247 -0
  2007. build/lib/nabu/processing/tests/test_roll.py +63 -0
  2008. build/lib/nabu/processing/tests/test_rotation.py +83 -0
  2009. build/lib/nabu/processing/tests/test_transpose.py +72 -0
  2010. build/lib/nabu/processing/tests/test_unsharp.py +106 -0
  2011. build/lib/nabu/processing/transpose.py +126 -0
  2012. build/lib/nabu/processing/unsharp.py +79 -0
  2013. build/lib/nabu/processing/unsharp_cuda.py +53 -0
  2014. build/lib/nabu/processing/unsharp_opencl.py +75 -0
  2015. build/lib/nabu/reconstruction/__init__.py +3 -0
  2016. build/lib/nabu/reconstruction/cone.py +241 -0
  2017. build/lib/nabu/reconstruction/fbp.py +124 -0
  2018. build/lib/nabu/reconstruction/fbp_base.py +391 -0
  2019. build/lib/nabu/reconstruction/fbp_opencl.py +78 -0
  2020. build/lib/nabu/reconstruction/filtering.py +220 -0
  2021. build/lib/nabu/reconstruction/filtering_cuda.py +103 -0
  2022. build/lib/nabu/reconstruction/filtering_opencl.py +111 -0
  2023. build/lib/nabu/reconstruction/projection.py +240 -0
  2024. build/lib/nabu/reconstruction/reconstructor.py +174 -0
  2025. build/lib/nabu/reconstruction/reconstructor_cuda.py +44 -0
  2026. build/lib/nabu/reconstruction/rings.py +248 -0
  2027. build/lib/nabu/reconstruction/rings_cuda.py +322 -0
  2028. build/lib/nabu/reconstruction/sinogram.py +467 -0
  2029. build/lib/nabu/reconstruction/sinogram_cuda.py +250 -0
  2030. build/lib/nabu/reconstruction/sinogram_opencl.py +40 -0
  2031. build/lib/nabu/reconstruction/tests/__init__.py +1 -0
  2032. build/lib/nabu/reconstruction/tests/test_cone.py +308 -0
  2033. build/lib/nabu/reconstruction/tests/test_deringer.py +220 -0
  2034. build/lib/nabu/reconstruction/tests/test_fbp.py +252 -0
  2035. build/lib/nabu/reconstruction/tests/test_filtering.py +133 -0
  2036. build/lib/nabu/reconstruction/tests/test_halftomo.py +100 -0
  2037. build/lib/nabu/reconstruction/tests/test_projector.py +164 -0
  2038. build/lib/nabu/reconstruction/tests/test_reconstructor.py +93 -0
  2039. build/lib/nabu/reconstruction/tests/test_sino_normalization.py +85 -0
  2040. build/lib/nabu/resources/__init__.py +0 -0
  2041. build/lib/nabu/resources/cli/__init__.py +0 -0
  2042. build/lib/nabu/resources/cor.py +5 -0
  2043. build/lib/nabu/resources/dataset_analyzer.py +469 -0
  2044. build/lib/nabu/resources/gpu.py +169 -0
  2045. build/lib/nabu/resources/logger.py +130 -0
  2046. build/lib/nabu/resources/nxflatfield.py +217 -0
  2047. build/lib/nabu/resources/templates/__init__.py +0 -0
  2048. build/lib/nabu/resources/tests/__init__.py +0 -0
  2049. build/lib/nabu/resources/tests/test_nxflatfield.py +104 -0
  2050. build/lib/nabu/resources/tests/test_units.py +47 -0
  2051. build/lib/nabu/resources/utils.py +174 -0
  2052. build/lib/nabu/stitching/__init__.py +0 -0
  2053. build/lib/nabu/stitching/alignment.py +184 -0
  2054. build/lib/nabu/stitching/config.py +1286 -0
  2055. build/lib/nabu/stitching/definitions.py +6 -0
  2056. build/lib/nabu/stitching/frame_composition.py +155 -0
  2057. build/lib/nabu/stitching/overlap.py +373 -0
  2058. build/lib/nabu/stitching/sample_normalization.py +60 -0
  2059. build/lib/nabu/stitching/slurm_utils.py +204 -0
  2060. build/lib/nabu/stitching/tests/__init__.py +0 -0
  2061. build/lib/nabu/stitching/tests/test_alignment.py +99 -0
  2062. build/lib/nabu/stitching/tests/test_config.py +226 -0
  2063. build/lib/nabu/stitching/tests/test_frame_composition.py +180 -0
  2064. build/lib/nabu/stitching/tests/test_overlap.py +98 -0
  2065. build/lib/nabu/stitching/tests/test_sample_normalization.py +49 -0
  2066. build/lib/nabu/stitching/tests/test_slurm_utils.py +146 -0
  2067. build/lib/nabu/stitching/tests/test_utils.py +21 -0
  2068. build/lib/nabu/stitching/tests/test_z_stitching.py +1183 -0
  2069. build/lib/nabu/stitching/utils.py +563 -0
  2070. build/lib/nabu/stitching/z_stitching.py +2279 -0
  2071. build/lib/nabu/tests.py +51 -0
  2072. build/lib/nabu/testutils.py +375 -0
  2073. build/lib/nabu/thirdparty/__init__.py +0 -0
  2074. build/lib/nabu/thirdparty/algotom_convert_sino.py +276 -0
  2075. build/lib/nabu/thirdparty/pore3d_deringer_munch.py +108 -0
  2076. build/lib/nabu/thirdparty/tomocupy_remove_stripe.py +586 -0
  2077. build/lib/nabu/thirdparty/tomopy_phase.py +239 -0
  2078. build/lib/nabu/thirdparty/tomwer_load_flats_darks.py +162 -0
  2079. build/lib/nabu/utils.py +836 -0
  2080. nabu/__init__.py +1 -1
  2081. nabu/io/cast_volume.py +10 -2
  2082. nabu/stitching/config.py +2 -2
  2083. nabu/stitching/z_stitching.py +3 -1
  2084. {nabu-2024.1.0rc4.dist-info → nabu-2024.1.1.dist-info}/METADATA +1 -1
  2085. nabu-2024.1.1.dist-info/RECORD +2375 -0
  2086. {nabu-2024.1.0rc4.dist-info → nabu-2024.1.1.dist-info}/WHEEL +1 -1
  2087. nabu-2024.1.1.dist-info/top_level.txt +4 -0
  2088. nabu-2024.1.0rc4.dist-info/RECORD +0 -296
  2089. nabu-2024.1.0rc4.dist-info/top_level.txt +0 -2
  2090. {nabu/app/tests → build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app}/__init__.py +0 -0
  2091. {nabu-2024.1.0rc4.dist-info → nabu-2024.1.1.dist-info}/LICENSE +0 -0
  2092. {nabu-2024.1.0rc4.dist-info → nabu-2024.1.1.dist-info}/entry_points.txt +0 -0
@@ -0,0 +1,836 @@
1
+ from functools import partial
2
+ import os
3
+ import sys
4
+ from functools import partial, lru_cache
5
+ from itertools import product
6
+ import warnings
7
+ from time import time
8
+ import posixpath
9
+ import numpy as np
10
+
11
+
12
+ def nextpow2(N, dtype=np.int32):
13
+ return 2 ** np.ceil(np.log2(N)).astype(dtype)
14
+
15
+
16
+ def previouspow2(N, dtype=np.int32):
17
+ return 2 ** np.floor(np.log2(N)).astype(dtype)
18
+
19
+
20
+ def updiv(a, b):
21
+ return (a + (b - 1)) // b
22
+
23
+
24
+ def convert_index(idx, idx_max, default_val):
25
+ """
26
+ Convert an index (possibly negative or None) to a non-negative integer.
27
+
28
+ Parameters
29
+ ----------
30
+ idx: int or None
31
+ Index
32
+ idx_max: int
33
+ Maximum value (upper bound) for the index.
34
+ default_val: int
35
+ Default value if idx is None
36
+
37
+ Examples
38
+ ---------
39
+ Given an integer `M`, `J = convert_index(i, M, XX)` returns an integer in the
40
+ mathematical range [0, M] (or Python `range(0, M)`). `J` can then be used
41
+ to define an upper bound of a range.
42
+ """
43
+ if idx is None:
44
+ return default_val
45
+ if idx > idx_max:
46
+ return idx_max
47
+ if idx < 0:
48
+ return idx % idx_max
49
+ return idx
50
+
51
+
52
+ def get_folder_path(foldername=""):
53
+ _file_dir = os.path.dirname(os.path.realpath(__file__))
54
+ package_dir = _file_dir
55
+ return os.path.join(package_dir, foldername)
56
+
57
+
58
+ def get_cuda_srcfile(filename):
59
+ src_relpath = os.path.join("cuda", "src")
60
+ cuda_src_folder = get_folder_path(foldername=src_relpath)
61
+ return os.path.join(cuda_src_folder, filename)
62
+
63
+
64
+ def get_opencl_srcfile(filename):
65
+ src_relpath = os.path.join("opencl", "src")
66
+ src_folder = get_folder_path(foldername=src_relpath)
67
+ return os.path.join(src_folder, filename)
68
+
69
+
70
+ def get_resource_file(filename, subfolder=None):
71
+ subfolder = subfolder or []
72
+ relpath = os.path.join("resources", *subfolder)
73
+ abspath = get_folder_path(foldername=relpath)
74
+ return os.path.join(abspath, filename)
75
+
76
+
77
+ def get_available_threads():
78
+ try:
79
+ n_threads = len(os.sched_getaffinity(0))
80
+ except AttributeError:
81
+ n_threads = int(os.environ.get("SLURM_CPUS_PER_TASK", os.cpu_count()))
82
+ return n_threads
83
+
84
+
85
+ def is_writeable(location):
86
+ """
87
+ Return True if a file/location is writeable.
88
+ """
89
+ return os.access(location, os.W_OK)
90
+
91
+
92
+ def is_int(num, eps=1e-7):
93
+ return abs(num - int(num)) < eps
94
+
95
+
96
+ def _sizeof(Type):
97
+ """
98
+ return the size (in bytes) of a scalar type, like the C behavior
99
+ """
100
+ return np.dtype(Type).itemsize
101
+
102
+
103
+ def get_ftype(url):
104
+ """
105
+ return supposed filetype of an url
106
+ """
107
+ if hasattr(url, "file_path"):
108
+ return os.path.splitext(url.file_path())[-1].replace(".", "")
109
+ else:
110
+ return os.path.splitext(url)[-1].replace(".", "")
111
+
112
+
113
+ def get_2D_3D_shape(shape):
114
+ if len(shape) == 2:
115
+ return (1,) + shape
116
+ return shape
117
+
118
+
119
+ def get_subregion(sub_region):
120
+ ymin, ymax = None, None
121
+ if sub_region is None:
122
+ xmin, xmax, ymin, ymax = None, None, None, None
123
+ elif len(sub_region) == 2:
124
+ first_part, second_part = sub_region
125
+ if np.iterable(first_part) and np.iterable(second_part):
126
+ xmin, xmax = first_part
127
+ ymin, ymax = second_part
128
+ else:
129
+ xmin, xmax = sub_region
130
+ elif len(sub_region) == 4:
131
+ xmin, xmax, ymin, ymax = sub_region
132
+ else:
133
+ raise ValueError("Expected parameter in the form (a, b, c, d) or ((a, b), (c, d))")
134
+ return xmin, xmax, ymin, ymax
135
+
136
+
137
+ def get_3D_subregion(sub_region):
138
+ if sub_region is None:
139
+ xmin, xmax, ymin, ymax, zmin, zmax = None, None, None, None, None, None
140
+ elif len(sub_region) == 3:
141
+ first_part, second_part, third_part = sub_region
142
+ xmin, xmax = first_part
143
+ ymin, ymax = second_part
144
+ zmin, zmax = third_part
145
+ elif len(sub_region) == 6:
146
+ xmin, xmax, ymin, ymax, zmin, zmax = sub_region
147
+ else:
148
+ raise ValueError(
149
+ "Expected parameter in the form (xmin, xmax, ymin, ymax, zmin, zmax) or ((xmin, xmax), (ymin, ymax), (zmin, zmax))"
150
+ )
151
+ return xmin, xmax, ymin, ymax, zmin, zmax
152
+
153
+
154
+ def to_3D_array(arr):
155
+ """
156
+ Turn an array to a (C-Contiguous) 3D array with the layout (n_arrays, n_y, n_x).
157
+ """
158
+ if arr.ndim == 3:
159
+ return arr
160
+ return np.tile(arr, (1, 1, 1))
161
+
162
+
163
+ def view_as_images_stack(img):
164
+ """
165
+ View an image (2D array) as a stack of one image (3D array).
166
+ No data is duplicated.
167
+ """
168
+ return img.reshape((1,) + img.shape)
169
+
170
+
171
+ def rescale_integers(items, new_tot):
172
+ """ "
173
+ From a given sequence of integers, create a new sequence
174
+ where the sum of all items must be equal to "new_tot".
175
+ The relative contribution of each item to the new total is approximately kept.
176
+
177
+ Parameters
178
+ ----------
179
+ items: array-like
180
+ Sequence of integers
181
+ new_tot: int
182
+ Integer indicating that the sum of the new array must be equal to this value
183
+ """
184
+ cur_items = np.array(items)
185
+ new_items = np.ceil(cur_items / cur_items.sum() * new_tot).astype(np.int64)
186
+ excess = new_items.sum() - new_tot
187
+ i = 0
188
+ while excess > 0:
189
+ ind = i % new_items.size
190
+ if cur_items[ind] > 0:
191
+ new_items[ind] -= 1
192
+ excess -= 1
193
+ i += 1
194
+ return new_items.tolist()
195
+
196
+
197
+ def merged_shape(shapes, axis=0):
198
+ n_img = sum(shape[axis] for shape in shapes)
199
+ if axis == 0:
200
+ return (n_img,) + shapes[0][1:]
201
+ elif axis == 1:
202
+ return (shapes[0][0], n_img, shapes[0][2])
203
+ elif axis == 2:
204
+ return shapes[0][:2] + (n_img,)
205
+
206
+
207
+ def is_device_backend(backend):
208
+ return backend.lower() in ["cuda", "opencl"]
209
+
210
+
211
+ def get_decay(curve, cutoff=1e3, vmax=None):
212
+ """
213
+ Assuming a decreasing curve, get the first point below a certain threshold.
214
+
215
+ Parameters
216
+ ----------
217
+ curve: numpy.ndarray
218
+ A 1D array
219
+ cutoff: float, optional
220
+ Threshold. Default is 1000.
221
+ vmax: float, optional
222
+ Curve maximum value
223
+ """
224
+ if vmax is None:
225
+ vmax = curve.max()
226
+ return np.argmax(np.abs(curve) < vmax / cutoff)
227
+
228
+
229
+ @lru_cache(maxsize=1)
230
+ def generate_powers():
231
+ """
232
+ Generate a list of powers of [2, 3, 5, 7],
233
+ up to (2**15)*(3**9)*(5**6)*(7**5).
234
+ """
235
+ primes = [2, 3, 5, 7]
236
+ maxpow = {2: 15, 3: 9, 5: 6, 7: 5}
237
+ valuations = []
238
+ for prime in primes:
239
+ # disallow any odd number (for R2C transform), and any number
240
+ # not multiple of 4 (Ram-Lak filter behaves strangely when
241
+ # dwidth_padded/2 is not even)
242
+ minval = 2 if prime == 2 else 0
243
+ valuations.append(range(minval, maxpow[prime] + 1))
244
+ powers = product(*valuations)
245
+ res = []
246
+ for pw in powers:
247
+ res.append(np.prod(list(map(lambda x: x[0] ** x[1], zip(primes, pw)))))
248
+ return np.unique(res)
249
+
250
+
251
+ def calc_padding_lengths1D(length, length_padded):
252
+ """
253
+ Compute the padding lengths at both side along one dimension.
254
+
255
+ Parameters
256
+ ----------
257
+ length: int
258
+ Number of elements along one dimension of the original array
259
+ length_padded: tuple
260
+ Number of elements along one dimension of the padded array
261
+
262
+ Returns
263
+ -------
264
+ pad_lengths: tuple
265
+ A tuple under the form (padding_left, padding_right). These are the
266
+ lengths needed to pad the original array.
267
+ """
268
+ pad_left = (length_padded - length) // 2
269
+ pad_right = length_padded - length - pad_left
270
+ return (pad_left, pad_right)
271
+
272
+
273
+ def calc_padding_lengths(shape, shape_padded):
274
+ """
275
+ Multi-dimensional version of calc_padding_lengths1D.
276
+ Please refer to the documentation of calc_padding_lengths1D.
277
+ """
278
+ assert len(shape) == len(shape_padded)
279
+ padding_lengths = []
280
+ for dim_len, dim_len_padded in zip(shape, shape_padded):
281
+ pad0, pad1 = calc_padding_lengths1D(dim_len, dim_len_padded)
282
+ padding_lengths.append((pad0, pad1))
283
+ return tuple(padding_lengths)
284
+
285
+
286
+ def partition_dict(dict_, n_partitions):
287
+ keys = np.sort(list(dict_.keys()))
288
+ res = []
289
+ for keys_arr in np.array_split(keys, n_partitions):
290
+ d = {}
291
+ for key in keys_arr:
292
+ d[key] = dict_[key]
293
+ res.append(d)
294
+ return res
295
+
296
+
297
+ def subsample_dict(dic, subsampling_factor):
298
+ """
299
+ Subsample a dict where keys are integers.
300
+ """
301
+ res = {}
302
+ indices = sorted(dic.keys())
303
+ for i in indices[::subsampling_factor]:
304
+ res[i] = dic[i]
305
+ return res
306
+
307
+
308
+ def compare_dicts(dic1, dic2):
309
+ """
310
+ Compare two dictionaries. Return None if and only iff the dictionaries are the same.
311
+
312
+ Parameters
313
+ ----------
314
+ dic1: dict
315
+ First dictionary
316
+ dic2: dict
317
+ Second dictionary
318
+
319
+ Returns
320
+ -------
321
+ res: result which can be the following:
322
+
323
+ - None: it means that dictionaries are the same
324
+ - empty string (""): the dictionaries do not have the same keys
325
+ - nonempty string: path to the first differing items
326
+ """
327
+ if set(dic1.keys()) != set(dic2.keys()):
328
+ return ""
329
+ for key, val1 in dic1.items():
330
+ val2 = dic2[key]
331
+ if isinstance(val1, dict):
332
+ res = compare_dicts(val1, val2)
333
+ if res is not None:
334
+ return posixpath.join(key, res)
335
+ # str
336
+ elif isinstance(val1, str):
337
+ if val1 != val2:
338
+ return key
339
+ # Scalars
340
+ elif np.isscalar(val1):
341
+ if not np.isclose(val1, val2):
342
+ return key
343
+ # NoneType
344
+ elif val1 is None:
345
+ if val2 is not None:
346
+ return key
347
+ # Array-like
348
+ elif np.iterable(val1):
349
+ arr1 = np.array(val1)
350
+ arr2 = np.array(val2)
351
+ if arr1.ndim != arr2.ndim or arr1.dtype != arr2.dtype or not np.allclose(arr1, arr2):
352
+ return key
353
+ else:
354
+ raise ValueError("Don't know what to do with type %s" % str(type(val1)))
355
+ return None
356
+
357
+
358
+ def remove_items_from_list(list_, items_to_remove):
359
+ """
360
+ Remove items from a list and return the removed elements.
361
+
362
+ Parameters
363
+ ----------
364
+ list_: list
365
+ List containing items to remove
366
+ items_to_remove: list
367
+ List of items to remove
368
+
369
+ Returns
370
+ --------
371
+ reduced_list: list
372
+ List with removed items
373
+ removed_items: dict
374
+ Dictionary where the keys are the indices of removed items, and values are the items
375
+ """
376
+ removed_items = {}
377
+ res = []
378
+ for i, val in enumerate(list_):
379
+ if val in items_to_remove:
380
+ removed_items[i] = val
381
+ else:
382
+ res.append(val)
383
+ return res, removed_items
384
+
385
+
386
+ def restore_items_in_list(list_, removed_items):
387
+ """
388
+ Undo the effect of the function `remove_items_from_list`
389
+
390
+ Parameters
391
+ ----------
392
+ list_: list
393
+ List where items were removed
394
+ removed_items: dict
395
+ Dictionary where the keys are the indices of removed items, and values are the items
396
+ """
397
+ for idx, val in removed_items.items():
398
+ list_.insert(idx, val)
399
+
400
+
401
+ def check_supported(param_value, available, param_desc):
402
+ if param_value not in available:
403
+ raise ValueError("Unsupported %s '%s'. Available are: %s" % (param_desc, param_value, str(available)))
404
+
405
+
406
+ def check_supported_enum(param_value, enum_cls, param_desc):
407
+ available = enum_cls.values()
408
+ return check_supported(param_value, available, param_desc)
409
+
410
+
411
+ def check_shape(shape, expected_shape, name):
412
+ if shape != expected_shape:
413
+ raise ValueError("Expected %s shape %s but got %s" % (name, str(expected_shape), str(shape)))
414
+
415
+
416
+ def copy_dict_items(dict_, keys):
417
+ """
418
+ Perform a shallow copy of a subset of a dictionary.
419
+ The subset if done by a list of keys.
420
+ """
421
+ res = {key: dict_[key] for key in keys}
422
+ return res
423
+
424
+
425
+ def remove_first_dict_items(dict_, n_items, sort_func=None, inplace=True):
426
+ """
427
+ Remove the first items of a dictionary. The keys have to be sortable
428
+ """
429
+ sorted_keys = sorted(dict_.keys(), key=sort_func)
430
+ if inplace:
431
+ for key in sorted_keys[:n_items]:
432
+ dict_.pop(key)
433
+ return dict_
434
+ else:
435
+ return copy_dict_items(dict_, sorted_keys[n_items:])
436
+
437
+
438
+ def recursive_copy_dict(dict_):
439
+ """
440
+ Perform a shallow copy of a dictionary of dictionaries.
441
+ This is NOT a deep copy ! Only reference to objects are kept.
442
+ """
443
+ if not (isinstance(dict_, dict)):
444
+ res = dict_
445
+ else:
446
+ res = {k: recursive_copy_dict(v) for k, v in dict_.items()}
447
+ return res
448
+
449
+
450
+ def subdivide_into_overlapping_segment(N, window_width, half_overlap):
451
+ """
452
+ Divide a segment into a number of possibly-overlapping sub-segments.
453
+
454
+ Parameters
455
+ ----------
456
+ N: int
457
+ Total segment length
458
+ window_width: int
459
+ Length of each segment
460
+ half_overlap: int
461
+ Half-length of the overlap between each sub-segment.
462
+
463
+ Returns
464
+ -------
465
+ segments: list
466
+ A list where each item is in the form
467
+ (left_margin_start, inner_segment_start, inner_segment_end, right_margin_end)
468
+ """
469
+ if half_overlap > 0 and half_overlap >= window_width // 2:
470
+ raise ValueError("overlap must be smaller than window_width")
471
+ w_in = window_width - 2 * half_overlap
472
+ n_segments = N // w_in
473
+ inner_start = w_in * np.arange(n_segments)
474
+ inner_end = w_in * (np.arange(n_segments) + 1)
475
+ margin_left_start = np.maximum(inner_start - half_overlap, 0)
476
+ margin_right_end = np.minimum(inner_end + half_overlap, N)
477
+ segments = [
478
+ (left_start, i_start, i_end, right_end)
479
+ for left_start, i_start, i_end, right_end in zip(
480
+ margin_left_start.tolist(), inner_start.tolist(), inner_end.tolist(), margin_right_end.tolist()
481
+ )
482
+ ]
483
+ if N % w_in:
484
+ # additional sub-segment
485
+ new_margin_left_start = inner_end[-1] - half_overlap
486
+ new_inner_start = inner_end[-1]
487
+ new_inner_end = N
488
+ segments.append((new_margin_left_start, new_inner_start, new_inner_end, new_inner_end))
489
+ return segments
490
+
491
+
492
+ def get_num_threads(n=None):
493
+ """
494
+ Get a number of threads (ex. to be used by fftw). If the argument is None, returns the total number of CPU threads.
495
+ If the argument is negative, the total number of available threads plus this number is returned.
496
+
497
+ Parameters
498
+ -----------
499
+ n: int, optional
500
+ - If an positive integer `n` is provided, then `n` threads are used
501
+ - If a negative integer `n` is provided, then `n_avail + n` threads are used
502
+ (so -1 to use all available threads minus one)
503
+ """
504
+ n_avail = get_available_threads()
505
+ if n is None or n == 0:
506
+ return n_avail
507
+ if n < 0:
508
+ return max(1, n_avail + n)
509
+ else:
510
+ return min(n_avail, n)
511
+
512
+
513
+ class DictToObj(object):
514
+ """utility class to transform a dictionary into an object with dictionary items as members.
515
+ Example:
516
+
517
+ >>> a=DictToObj( dict(i=1,j=1))
518
+ ... a.j+a.i
519
+
520
+ """
521
+
522
+ def __init__(self, dictio):
523
+ self.__dict__ = dictio
524
+
525
+
526
+ def remove_parenthesis_or_brackets(input_str):
527
+ """
528
+ clear string from left and or roght parenthesis / braquets
529
+ """
530
+ if input_str.startswith("(") and input_str.endswith(")") or input_str.startswith("[") and input_str.endswith("]"):
531
+ input_str = input_str[1:-1]
532
+ return input_str
533
+
534
+
535
+ def filter_str_def(elmt):
536
+ """clean elemt if is a string defined from a text file.
537
+ Remove some character that could have be put on left or right and some empty spaces"""
538
+ if elmt is None:
539
+ return None
540
+ assert isinstance(elmt, str)
541
+ elmt = elmt.lstrip(" ").rstrip(" ")
542
+ elmt = elmt.lstrip("'").lstrip('"')
543
+ elmt = elmt.rstrip("'").rstrip('"')
544
+ elmt = elmt.lstrip(" ").rstrip(" ")
545
+ for character in ("'", '"'):
546
+ if elmt.startswith(character) and elmt.endswith(character):
547
+ elmt = elmt[1:-1]
548
+ return elmt
549
+
550
+
551
+ def convert_str_to_tuple(input_str: str, none_if_empty: bool = False):
552
+ """
553
+ :param str input_str: string to convert
554
+ :param bool none_if_empty: if true and the conversion is an empty tuple
555
+ return None instead of an empty tuple
556
+ """
557
+ if isinstance(input_str, tuple):
558
+ return input_str
559
+ if not isinstance(input_str, str):
560
+ raise TypeError("input_str should be a string not {}, {}".format(type(input_str), input_str))
561
+ input_str = input_str.lstrip(" ").lstrip("(").lstrip("[").lstrip(" ").rstrip(" ")
562
+ input_str = remove_parenthesis_or_brackets(input_str)
563
+ input_str = input_str.replace("\n", ",")
564
+
565
+ elmts = input_str.split(",")
566
+ elmts = [filter_str_def(elmt) for elmt in elmts]
567
+ rm_empty_str = lambda a: a != ""
568
+ elmts = list(filter(rm_empty_str, elmts))
569
+ if none_if_empty and len(elmts) == 0:
570
+ return None
571
+ else:
572
+ return tuple(elmts)
573
+
574
+
575
+ class Progress:
576
+ """Simple interface for defining advancement on a 100 percentage base"""
577
+
578
+ def __init__(self, name: str):
579
+ self._name = name
580
+ self.set_name(name)
581
+
582
+ def set_name(self, name):
583
+ self._name = name
584
+ self.reset()
585
+
586
+ def reset(self, max_=None):
587
+ """
588
+ reset the advancement to n and max advancement to max_
589
+ :param int max_:
590
+ """
591
+ self._n_processed = 0
592
+ self._max_processed = max_
593
+
594
+ def start_process(self) -> None:
595
+ self.set_advancement(0)
596
+
597
+ def set_advancement(self, value: int) -> None:
598
+ """
599
+
600
+ :param int value: set advancement to value
601
+ """
602
+ length = 20 # modify this to change the length
603
+ block = int(round(length * value / 100))
604
+ blocks_str = "#" * block + "-" * (length - block)
605
+ msg = "\r{0}: [{1}] {2}%".format(self._name, blocks_str, round(value, 2))
606
+ if value >= 100:
607
+ msg += " DONE\r\n"
608
+ sys.stdout.write(msg)
609
+ sys.stdout.flush()
610
+
611
+ def end_process(self) -> None:
612
+ """Set advancement to 100 %"""
613
+ self.set_advancement(100)
614
+
615
+ def set_max_advancement(self, n: int) -> None:
616
+ """
617
+
618
+ :param int n: number of steps contained by the advancement. When
619
+ advancement reach this value, advancement will be 100 %
620
+ """
621
+ self._max_processed = n
622
+
623
+ def increase_advancement(self, i: int = 1) -> None:
624
+ """
625
+
626
+ :param int i: increase the advancement of n step
627
+ """
628
+ self._n_processed += i
629
+ advancement = int(float(self._n_processed / self._max_processed) * 100)
630
+ self.set_advancement(advancement)
631
+
632
+
633
+ def concatenate_dict(dict_1, dict_2) -> dict:
634
+ """update dict which has dict as values. And we want concatenate those values to"""
635
+ res = dict_1.copy()
636
+ for key in dict_2:
637
+ if key in dict_1:
638
+ res[key].update(dict_2[key])
639
+ else:
640
+ res[key] = dict_2[key]
641
+ return res
642
+
643
+
644
+ class BaseClassError:
645
+ def __init__(self, *args, **kwargs):
646
+ raise ValueError("Base class")
647
+
648
+
649
+ def MissingComponentError(msg):
650
+ class MissingComponentCls:
651
+ def __init__(self, *args, **kwargs):
652
+ raise RuntimeError(msg)
653
+
654
+ return MissingComponentCls
655
+
656
+
657
+ # ------------------------------------------------------------------------------
658
+ # ------------------------ Image (move elsewhere ?) ----------------------------
659
+ # ------------------------------------------------------------------------------
660
+
661
+
662
+ def generate_coords(img_shp, center=None):
663
+ l_r, l_c = float(img_shp[0]), float(img_shp[1])
664
+ R, C = np.mgrid[:l_r, :l_c] # np.indices is faster
665
+ if center is None:
666
+ center0, center1 = l_r / 2.0, l_c / 2.0
667
+ else:
668
+ center0, center1 = center
669
+ R += 0.5 - center0
670
+ C += 0.5 - center1
671
+ return R, C
672
+
673
+
674
+ def clip_circle(img, center=None, radius=None):
675
+ R, C = generate_coords(img.shape, center)
676
+ if radius is None:
677
+ radius = R.shape[-1] // 2
678
+ M = R**2 + C**2
679
+ res = np.zeros_like(img)
680
+ res[M < radius**2] = img[M < radius**2]
681
+ return res
682
+
683
+
684
+ def extend_image_onepixel(img):
685
+ # extend of one pixel
686
+ img2 = np.zeros((img.shape[0] + 2, img.shape[1] + 2), dtype=img.dtype)
687
+ img2[0, 1:-1] = img[0]
688
+ img2[-1, 1:-1] = img[-1]
689
+ img2[1:-1, 0] = img[:, 0]
690
+ img2[1:-1, -1] = img[:, -1]
691
+ # middle
692
+ img2[1:-1, 1:-1] = img
693
+ # corners
694
+ img2[0, 0] = img[0, 0]
695
+ img2[-1, 0] = img[-1, 0]
696
+ img2[0, -1] = img[0, -1]
697
+ img2[-1, -1] = img[-1, -1]
698
+ return img2
699
+
700
+
701
+ def median2(img):
702
+ """
703
+ 3x3 median filter for 2D arrays, with "reflect" boundary mode.
704
+ Roughly same speed as scipy median filter, but more memory demanding.
705
+ """
706
+ img2 = extend_image_onepixel(img)
707
+ I = np.array(
708
+ [
709
+ img2[0:-2, 0:-2],
710
+ img2[0:-2, 1:-1],
711
+ img2[0:-2, 2:],
712
+ img2[1:-1, 0:-2],
713
+ img2[1:-1, 1:-1],
714
+ img2[1:-1, 2:],
715
+ img2[2:, 0:-2],
716
+ img2[2:, 1:-1],
717
+ img2[2:, 2:],
718
+ ]
719
+ )
720
+ return np.median(I, axis=0)
721
+
722
+
723
+ # ------------------------------------------------------------------------------
724
+ # ---------------------------- Decorators --------------------------------------
725
+ # ------------------------------------------------------------------------------
726
+
727
+ _warnings = {}
728
+
729
+
730
+ def measure_time(func):
731
+ def wrapper(*args, **kwargs):
732
+ t0 = time()
733
+ res = func(*args, **kwargs)
734
+ el = time() - t0
735
+ return el, res
736
+
737
+ return wrapper
738
+
739
+
740
+ def wip(func):
741
+ def wrapper(*args, **kwargs):
742
+ func_name = func.__name__
743
+ if func_name not in _warnings:
744
+ _warnings[func_name] = 1
745
+ print("Warning: function %s is a work in progress, it is likely to change in the future")
746
+ return func(*args, **kwargs)
747
+
748
+ return wrapper
749
+
750
+
751
+ def warning(msg):
752
+ def decorator(func):
753
+ def wrapper(*args, **kwargs):
754
+ func_name = func.__name__
755
+ if func_name not in _warnings:
756
+ _warnings[func_name] = 1
757
+ print(msg)
758
+ res = func(*args, **kwargs)
759
+ return res
760
+
761
+ return wrapper
762
+
763
+ return decorator
764
+
765
+
766
+ def deprecated(msg, do_print=False):
767
+ def decorator(func):
768
+ def wrapper(*args, **kwargs):
769
+ deprecation_warning(msg, do_print=do_print, func_name=func.__name__)
770
+ res = func(*args, **kwargs)
771
+ return res
772
+
773
+ return wrapper
774
+
775
+ return decorator
776
+
777
+
778
+ def deprecated_class(msg, do_print=False):
779
+ def decorator(cls):
780
+ class wrapper:
781
+ def __init__(self, *args, **kwargs):
782
+ deprecation_warning(msg, do_print=do_print, func_name=cls.__name__)
783
+ self.wrapped = cls(*args, **kwargs)
784
+
785
+ # This is so ugly :-(
786
+ def __getattr__(self, name):
787
+ return getattr(self.wrapped, name)
788
+
789
+ return wrapper
790
+
791
+ return decorator
792
+
793
+
794
+ def deprecation_warning(message, do_print=True, func_name=None):
795
+ func_name_msg = str("%s: " % func_name) if func_name is not None else ""
796
+ func_name = func_name or "None"
797
+ if _warnings.get(func_name, False):
798
+ return
799
+ warnings.warn(message, DeprecationWarning)
800
+ if do_print:
801
+ print("Deprecation warning: %s%s" % (func_name_msg, message))
802
+ _warnings[func_name] = 1
803
+
804
+
805
+ def _docstring(dest, origin):
806
+ """Implementation of docstring decorator.
807
+
808
+ It patches dest.__doc__.
809
+ """
810
+ if not isinstance(dest, type) and isinstance(origin, type):
811
+ # func is not a class, but origin is, get the method with the same name
812
+ try:
813
+ origin = getattr(origin, dest.__name__)
814
+ except AttributeError:
815
+ raise ValueError("origin class has no %s method" % dest.__name__)
816
+
817
+ dest.__doc__ = origin.__doc__
818
+ return dest
819
+
820
+
821
+ def docstring(origin):
822
+ """Decorator to initialize the docstring from another source.
823
+
824
+ This is useful to duplicate a docstring for inheritance and composition.
825
+
826
+ If origin is a method or a function, it copies its docstring.
827
+ If origin is a class, the docstring is copied from the method
828
+ of that class which has the same name as the method/function
829
+ being decorated.
830
+
831
+ :param origin:
832
+ The method, function or class from which to get the docstring
833
+ :raises ValueError:
834
+ If the origin class has not method n case the
835
+ """
836
+ return partial(_docstring, origin=origin)