nabu 2022.3.0a1__py3-none-any.whl → 2023.1.0a2__py3-none-any.whl

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Files changed (96) hide show
  1. nabu/__init__.py +1 -1
  2. nabu/app/bootstrap.py +7 -1
  3. nabu/app/cast_volume.py +8 -2
  4. nabu/app/cli_configs.py +69 -0
  5. nabu/app/composite_cor.py +97 -0
  6. nabu/app/create_distortion_map_from_poly.py +118 -0
  7. nabu/app/nx_z_splitter.py +1 -1
  8. nabu/app/prepare_weights_double.py +21 -16
  9. nabu/app/reconstruct_helical.py +0 -1
  10. nabu/app/utils.py +10 -5
  11. nabu/cuda/processing.py +1 -0
  12. nabu/cuda/tests/test_padding.py +1 -0
  13. nabu/cuda/utils.py +1 -0
  14. nabu/distributed/__init__.py +0 -0
  15. nabu/distributed/utils.py +57 -0
  16. nabu/distributed/worker.py +543 -0
  17. nabu/estimation/cor.py +3 -7
  18. nabu/estimation/cor_sino.py +2 -1
  19. nabu/estimation/distortion.py +6 -4
  20. nabu/io/cast_volume.py +10 -1
  21. nabu/io/detector_distortion.py +305 -0
  22. nabu/io/reader.py +37 -7
  23. nabu/io/reader_helical.py +0 -3
  24. nabu/io/tests/test_cast_volume.py +16 -4
  25. nabu/io/tests/test_detector_distortion.py +178 -0
  26. nabu/io/tests/test_writers.py +2 -2
  27. nabu/io/tiffwriter_zmm.py +2 -3
  28. nabu/io/writer.py +84 -1
  29. nabu/io/writer_BACKUP_193259.py +556 -0
  30. nabu/io/writer_BACKUP_193381.py +556 -0
  31. nabu/io/writer_BASE_193259.py +548 -0
  32. nabu/io/writer_BASE_193381.py +548 -0
  33. nabu/io/writer_LOCAL_193259.py +550 -0
  34. nabu/io/writer_LOCAL_193381.py +550 -0
  35. nabu/io/writer_REMOTE_193259.py +557 -0
  36. nabu/io/writer_REMOTE_193381.py +557 -0
  37. nabu/misc/fourier_filters.py +2 -0
  38. nabu/misc/rotation.py +0 -1
  39. nabu/misc/tests/test_rotation.py +1 -0
  40. nabu/pipeline/config_validators.py +10 -0
  41. nabu/pipeline/datadump.py +1 -1
  42. nabu/pipeline/dataset_validator.py +0 -1
  43. nabu/pipeline/detector_distortion_provider.py +20 -0
  44. nabu/pipeline/estimators.py +35 -21
  45. nabu/pipeline/fallback_utils.py +1 -1
  46. nabu/pipeline/fullfield/chunked.py +30 -15
  47. nabu/pipeline/fullfield/chunked_black.py +881 -0
  48. nabu/pipeline/fullfield/chunked_cuda.py +34 -4
  49. nabu/pipeline/fullfield/chunked_fb.py +966 -0
  50. nabu/pipeline/fullfield/chunked_google.py +921 -0
  51. nabu/pipeline/fullfield/chunked_pep8.py +920 -0
  52. nabu/pipeline/fullfield/computations.py +7 -6
  53. nabu/pipeline/fullfield/dataset_validator.py +1 -1
  54. nabu/pipeline/fullfield/grouped_cuda.py +6 -0
  55. nabu/pipeline/fullfield/nabu_config.py +15 -3
  56. nabu/pipeline/fullfield/processconfig.py +5 -0
  57. nabu/pipeline/fullfield/reconstruction.py +1 -2
  58. nabu/pipeline/helical/gridded_accumulator.py +1 -8
  59. nabu/pipeline/helical/helical_chunked_regridded.py +48 -33
  60. nabu/pipeline/helical/helical_reconstruction.py +1 -9
  61. nabu/pipeline/helical/nabu_config.py +11 -14
  62. nabu/pipeline/helical/span_strategy.py +11 -4
  63. nabu/pipeline/helical/tests/test_accumulator.py +0 -3
  64. nabu/pipeline/helical/tests/test_pipeline_elements_full.py +0 -6
  65. nabu/pipeline/helical/tests/test_strategy.py +0 -1
  66. nabu/pipeline/helical/weight_balancer.py +0 -1
  67. nabu/pipeline/params.py +4 -0
  68. nabu/pipeline/processconfig.py +6 -2
  69. nabu/pipeline/writer.py +9 -4
  70. nabu/preproc/distortion.py +4 -3
  71. nabu/preproc/double_flatfield.py +16 -4
  72. nabu/preproc/double_flatfield_cuda.py +3 -2
  73. nabu/preproc/double_flatfield_variable_region.py +13 -4
  74. nabu/preproc/flatfield.py +29 -7
  75. nabu/preproc/flatfield_cuda.py +0 -1
  76. nabu/preproc/flatfield_variable_region.py +5 -2
  77. nabu/preproc/phase.py +0 -1
  78. nabu/preproc/phase_cuda.py +0 -1
  79. nabu/preproc/tests/test_ctf.py +4 -3
  80. nabu/preproc/tests/test_flatfield.py +6 -7
  81. nabu/reconstruction/fbp_opencl.py +1 -1
  82. nabu/reconstruction/filtering.py +0 -1
  83. nabu/reconstruction/tests/test_fbp.py +1 -0
  84. nabu/resources/dataset_analyzer.py +0 -1
  85. nabu/resources/templates/bm05_pag.conf +34 -0
  86. nabu/resources/templates/id16_ctf.conf +2 -1
  87. nabu/resources/tests/test_nxflatfield.py +0 -1
  88. nabu/resources/tests/test_units.py +0 -1
  89. nabu/stitching/frame_composition.py +7 -1
  90. {nabu-2022.3.0a1.dist-info → nabu-2023.1.0a2.dist-info}/METADATA +2 -7
  91. {nabu-2022.3.0a1.dist-info → nabu-2023.1.0a2.dist-info}/RECORD +96 -75
  92. {nabu-2022.3.0a1.dist-info → nabu-2023.1.0a2.dist-info}/WHEEL +1 -1
  93. {nabu-2022.3.0a1.dist-info → nabu-2023.1.0a2.dist-info}/entry_points.txt +2 -1
  94. {nabu-2022.3.0a1.dist-info → nabu-2023.1.0a2.dist-info}/LICENSE +0 -0
  95. {nabu-2022.3.0a1.dist-info → nabu-2023.1.0a2.dist-info}/top_level.txt +0 -0
  96. {nabu-2022.3.0a1.dist-info → nabu-2023.1.0a2.dist-info}/zip-safe +0 -0
nabu/pipeline/fullfield/chunked_cuda.py CHANGED
@@ -43,10 +43,34 @@ class CudaChunkedPipeline(ChunkedPipeline):
43
43
  HistogramClass = CudaPartialHistogram
44
44
  SinoNormalizationClass = CudaSinoNormalization
45
45
 
46
- def __init__(self, process_config, chunk_shape, logger=None, extra_options=None, margin=None, cuda_options=None):
46
+ def __init__(
47
+ self,
48
+ process_config,
49
+ chunk_shape,
50
+ logger=None,
51
+ extra_options=None,
52
+ margin=None,
53
+ use_grouped_mode=False,
54
+ cuda_options=None,
55
+ ):
47
56
  self._init_cuda(cuda_options)
48
- super().__init__(process_config, chunk_shape, logger=logger, extra_options=extra_options, margin=margin)
57
+ super().__init__(
58
+ process_config,
59
+ chunk_shape,
60
+ logger=logger,
61
+ extra_options=extra_options,
62
+ use_grouped_mode=use_grouped_mode,
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+ margin=margin,
64
+ )
49
65
  self._allocate_array(self.radios.shape, "f", name="radios")
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+ self._determine_when_to_transfer_data_on_gpu()
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+
68
+ def _determine_when_to_transfer_data_on_gpu(self):
69
+ # Decide when to transfer data to GPU. Normally it's right after reading the data,
70
+ # But sometimes a part of the processing is done on CPU.
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+ self._when_to_transfer_radios_on_gpu = "read_data"
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+ if self.flatfield is not None and self.flatfield.distortion_correction is not None:
73
+ self._when_to_transfer_radios_on_gpu = "flatfield"
50
74
 
51
75
  def _init_cuda(self, cuda_options):
52
76
  if not (__has_pycuda__):
@@ -68,6 +92,7 @@ class CudaChunkedPipeline(ChunkedPipeline):
68
92
  return d_arr
69
93
 
70
94
  def _transfer_radios_to_gpu(self):
95
+ self.logger.debug("Transfering radios to GPU")
71
96
  self._d_radios.set(self.radios)
72
97
  self._h_radios = self.radios
73
98
  self.radios = self._d_radios
@@ -81,8 +106,13 @@ class CudaChunkedPipeline(ChunkedPipeline):
81
106
 
82
107
  def _read_data(self):
83
108
  super()._read_data()
84
- self.logger.debug("Transfering radios to GPU")
85
- self._transfer_radios_to_gpu()
109
+ if self._when_to_transfer_radios_on_gpu == "read_data":
110
+ self._transfer_radios_to_gpu()
111
+
112
+ def _flatfield(self):
113
+ super()._flatfield()
114
+ if self._when_to_transfer_radios_on_gpu == "flatfield":
115
+ self._transfer_radios_to_gpu()
86
116
 
87
117
  def _reconstruct(self):
88
118
  super()._reconstruct()