nabu 2024.1.9__py3-none-any.whl → 2024.2.0__py3-none-any.whl

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Files changed (151) hide show
  1. nabu/__init__.py +1 -1
  2. nabu/app/bootstrap.py +2 -3
  3. nabu/app/cast_volume.py +4 -2
  4. nabu/app/cli_configs.py +5 -0
  5. nabu/app/composite_cor.py +1 -1
  6. nabu/app/create_distortion_map_from_poly.py +5 -6
  7. nabu/app/diag_to_pix.py +7 -19
  8. nabu/app/diag_to_rot.py +14 -29
  9. nabu/app/double_flatfield.py +32 -44
  10. nabu/app/parse_reconstruction_log.py +3 -0
  11. nabu/app/reconstruct.py +53 -15
  12. nabu/app/reconstruct_helical.py +2 -2
  13. nabu/app/stitching.py +27 -13
  14. nabu/app/tests/test_reduce_dark_flat.py +4 -1
  15. nabu/cuda/kernel.py +11 -2
  16. nabu/cuda/processing.py +2 -2
  17. nabu/cuda/src/cone.cu +77 -0
  18. nabu/cuda/src/hierarchical_backproj.cu +271 -0
  19. nabu/cuda/utils.py +0 -6
  20. nabu/estimation/alignment.py +5 -19
  21. nabu/estimation/cor.py +173 -599
  22. nabu/estimation/cor_sino.py +356 -26
  23. nabu/estimation/focus.py +63 -11
  24. nabu/estimation/tests/test_cor.py +124 -58
  25. nabu/estimation/tests/test_focus.py +6 -6
  26. nabu/estimation/tilt.py +2 -1
  27. nabu/estimation/utils.py +5 -33
  28. nabu/io/__init__.py +1 -1
  29. nabu/io/cast_volume.py +1 -1
  30. nabu/io/reader.py +416 -21
  31. nabu/io/tests/test_readers.py +422 -0
  32. nabu/io/tests/test_writers.py +1 -102
  33. nabu/io/writer.py +4 -433
  34. nabu/opencl/kernel.py +14 -3
  35. nabu/opencl/processing.py +8 -0
  36. nabu/pipeline/config_validators.py +5 -2
  37. nabu/pipeline/datadump.py +12 -5
  38. nabu/pipeline/estimators.py +162 -188
  39. nabu/pipeline/fullfield/chunked.py +168 -92
  40. nabu/pipeline/fullfield/chunked_cuda.py +7 -3
  41. nabu/pipeline/fullfield/computations.py +2 -7
  42. nabu/pipeline/fullfield/dataset_validator.py +0 -4
  43. nabu/pipeline/fullfield/nabu_config.py +37 -13
  44. nabu/pipeline/fullfield/processconfig.py +22 -13
  45. nabu/pipeline/fullfield/reconstruction.py +13 -9
  46. nabu/pipeline/helical/helical_chunked_regridded.py +1 -1
  47. nabu/pipeline/helical/helical_chunked_regridded_cuda.py +1 -0
  48. nabu/pipeline/helical/helical_reconstruction.py +1 -1
  49. nabu/pipeline/params.py +21 -1
  50. nabu/pipeline/processconfig.py +1 -12
  51. nabu/pipeline/reader.py +146 -0
  52. nabu/pipeline/tests/test_estimators.py +44 -72
  53. nabu/pipeline/utils.py +4 -2
  54. nabu/pipeline/writer.py +10 -2
  55. nabu/preproc/ccd_cuda.py +1 -1
  56. nabu/preproc/ctf.py +14 -7
  57. nabu/preproc/ctf_cuda.py +2 -3
  58. nabu/preproc/double_flatfield.py +5 -12
  59. nabu/preproc/double_flatfield_cuda.py +2 -2
  60. nabu/preproc/flatfield.py +5 -1
  61. nabu/preproc/flatfield_cuda.py +5 -1
  62. nabu/preproc/phase.py +24 -73
  63. nabu/preproc/phase_cuda.py +5 -8
  64. nabu/preproc/tests/test_ctf.py +11 -7
  65. nabu/preproc/tests/test_flatfield.py +67 -122
  66. nabu/preproc/tests/test_paganin.py +54 -30
  67. nabu/processing/azim.py +206 -0
  68. nabu/processing/convolution_cuda.py +1 -1
  69. nabu/processing/fft_cuda.py +15 -17
  70. nabu/processing/histogram.py +2 -0
  71. nabu/processing/histogram_cuda.py +2 -1
  72. nabu/processing/kernel_base.py +3 -0
  73. nabu/processing/muladd_cuda.py +1 -0
  74. nabu/processing/padding_opencl.py +1 -1
  75. nabu/processing/roll_opencl.py +1 -0
  76. nabu/processing/rotation_cuda.py +2 -2
  77. nabu/processing/tests/test_fft.py +17 -10
  78. nabu/processing/unsharp_cuda.py +1 -1
  79. nabu/reconstruction/cone.py +104 -40
  80. nabu/reconstruction/fbp.py +3 -0
  81. nabu/reconstruction/fbp_base.py +7 -2
  82. nabu/reconstruction/filtering.py +20 -7
  83. nabu/reconstruction/filtering_cuda.py +7 -1
  84. nabu/reconstruction/hbp.py +424 -0
  85. nabu/reconstruction/mlem.py +99 -0
  86. nabu/reconstruction/reconstructor.py +2 -0
  87. nabu/reconstruction/rings_cuda.py +19 -19
  88. nabu/reconstruction/sinogram_cuda.py +1 -0
  89. nabu/reconstruction/sinogram_opencl.py +3 -1
  90. nabu/reconstruction/tests/test_cone.py +10 -5
  91. nabu/reconstruction/tests/test_deringer.py +7 -6
  92. nabu/reconstruction/tests/test_fbp.py +124 -10
  93. nabu/reconstruction/tests/test_filtering.py +13 -11
  94. nabu/reconstruction/tests/test_halftomo.py +30 -4
  95. nabu/reconstruction/tests/test_mlem.py +91 -0
  96. nabu/reconstruction/tests/test_reconstructor.py +8 -3
  97. nabu/resources/dataset_analyzer.py +142 -92
  98. nabu/resources/gpu.py +1 -0
  99. nabu/resources/nxflatfield.py +134 -125
  100. nabu/resources/templates/id16a_fluo.conf +42 -0
  101. nabu/resources/tests/test_extract.py +10 -0
  102. nabu/resources/tests/test_nxflatfield.py +2 -2
  103. nabu/stitching/alignment.py +80 -24
  104. nabu/stitching/config.py +105 -68
  105. nabu/stitching/definitions.py +1 -0
  106. nabu/stitching/frame_composition.py +68 -60
  107. nabu/stitching/overlap.py +91 -51
  108. nabu/stitching/single_axis_stitching.py +32 -0
  109. nabu/stitching/slurm_utils.py +6 -6
  110. nabu/stitching/stitcher/__init__.py +0 -0
  111. nabu/stitching/stitcher/base.py +124 -0
  112. nabu/stitching/stitcher/dumper/__init__.py +3 -0
  113. nabu/stitching/stitcher/dumper/base.py +94 -0
  114. nabu/stitching/stitcher/dumper/postprocessing.py +356 -0
  115. nabu/stitching/stitcher/dumper/preprocessing.py +60 -0
  116. nabu/stitching/stitcher/post_processing.py +555 -0
  117. nabu/stitching/stitcher/pre_processing.py +1068 -0
  118. nabu/stitching/stitcher/single_axis.py +484 -0
  119. nabu/stitching/stitcher/stitcher.py +0 -0
  120. nabu/stitching/stitcher/y_stitcher.py +13 -0
  121. nabu/stitching/stitcher/z_stitcher.py +45 -0
  122. nabu/stitching/stitcher_2D.py +278 -0
  123. nabu/stitching/tests/test_config.py +12 -37
  124. nabu/stitching/tests/test_frame_composition.py +33 -59
  125. nabu/stitching/tests/test_overlap.py +149 -7
  126. nabu/stitching/tests/test_utils.py +1 -1
  127. nabu/stitching/tests/test_y_preprocessing_stitching.py +132 -0
  128. nabu/stitching/tests/{test_z_stitching.py → test_z_postprocessing_stitching.py} +167 -561
  129. nabu/stitching/tests/test_z_preprocessing_stitching.py +431 -0
  130. nabu/stitching/utils/__init__.py +1 -0
  131. nabu/stitching/utils/post_processing.py +281 -0
  132. nabu/stitching/utils/tests/test_post-processing.py +21 -0
  133. nabu/stitching/{utils.py → utils/utils.py} +79 -52
  134. nabu/stitching/y_stitching.py +27 -0
  135. nabu/stitching/z_stitching.py +32 -2263
  136. nabu/testutils.py +1 -152
  137. nabu/thirdparty/tomocupy_remove_stripe.py +43 -9
  138. nabu/utils.py +158 -61
  139. {nabu-2024.1.9.dist-info → nabu-2024.2.0.dist-info}/METADATA +10 -3
  140. {nabu-2024.1.9.dist-info → nabu-2024.2.0.dist-info}/RECORD +144 -121
  141. nabu/io/tiffwriter_zmm.py +0 -99
  142. nabu/pipeline/fallback_utils.py +0 -149
  143. nabu/pipeline/helical/tests/test_accumulator.py +0 -158
  144. nabu/pipeline/helical/tests/test_pipeline_elements_full.py +0 -355
  145. nabu/pipeline/helical/tests/test_strategy.py +0 -61
  146. nabu/pipeline/helical/utils.py +0 -51
  147. nabu/pipeline/tests/test_chunk_reader.py +0 -74
  148. {nabu-2024.1.9.dist-info → nabu-2024.2.0.dist-info}/LICENSE +0 -0
  149. {nabu-2024.1.9.dist-info → nabu-2024.2.0.dist-info}/WHEEL +0 -0
  150. {nabu-2024.1.9.dist-info → nabu-2024.2.0.dist-info}/entry_points.txt +0 -0
  151. {nabu-2024.1.9.dist-info → nabu-2024.2.0.dist-info}/top_level.txt +0 -0
@@ -17,7 +17,6 @@ from nxtomo.nxobject.nxdetector import ImageKey
17
17
 
18
18
 
19
19
  class ProcessConfig(ProcessConfigBase):
20
-
21
20
  """
22
21
  A ProcessConfig object has these main fields:
23
22
  - dataset_info: information about the current dataset
@@ -57,7 +56,7 @@ class ProcessConfig(ProcessConfigBase):
57
56
  "flatfield",
58
57
  "ccd_correction",
59
58
  "double_flatfield",
60
- "rotate_projections",
59
+ "tilt_correction",
61
60
  "phase",
62
61
  "unsharp_mask",
63
62
  "take_log",
@@ -74,13 +73,16 @@ class ProcessConfig(ProcessConfigBase):
74
73
  Update the 'dataset_info' (DatasetAnalyzer class instance) data structure with options from user configuration.
75
74
  """
76
75
  self.logger.debug("Updating dataset information with user configuration")
77
- if self.dataset_info.kind == "hdf5":
76
+ if self.dataset_info.kind == "nx":
78
77
  update_dataset_info_flats_darks(
79
78
  self.dataset_info,
80
79
  self.nabu_config["preproc"]["flatfield"],
81
80
  output_dir=self.nabu_config["output"]["location"],
82
81
  darks_flats_dir=self.nabu_config["dataset"]["darks_flats_dir"],
83
82
  )
83
+ elif self.dataset_info.kind == "edf":
84
+ self.dataset_info.flats = self.dataset_info.get_reduced_flats()
85
+ self.dataset_info.darks = self.dataset_info.get_reduced_darks()
84
86
  self.rec_params = self.nabu_config["reconstruction"]
85
87
 
86
88
  subsampling_factor, subsampling_start = self.nabu_config["dataset"]["projections_subsampling"]
@@ -361,7 +363,6 @@ class ProcessConfig(ProcessConfigBase):
361
363
  method: str or None
362
364
  Rotation method: one of the values of `nabu.resources.params.radios_rotation_mode`
363
365
  """
364
- user_rotate_projections = self.nabu_config["preproc"]["rotate_projections"]
365
366
  tilt = self.dataset_info.detector_tilt
366
367
  phase_method = self.nabu_config["phase"]["method"]
367
368
  do_ctf = phase_method == "CTF"
@@ -369,7 +370,7 @@ class ProcessConfig(ProcessConfigBase):
369
370
  do_unsharp = (
370
371
  self.nabu_config["phase"]["unsharp_method"] is not None and self.nabu_config["phase"]["unsharp_coeff"] > 0
371
372
  )
372
- if user_rotate_projections is None and tilt is None:
373
+ if tilt is None:
373
374
  return None
374
375
  if do_ctf:
375
376
  return "full"
@@ -397,7 +398,6 @@ class ProcessConfig(ProcessConfigBase):
397
398
  # For now data is assumed to be on disk (see issue #66).
398
399
  tasks.append("read_chunk")
399
400
  options["read_chunk"] = {
400
- "files": dataset_info.projections,
401
401
  "sub_region": None,
402
402
  "binning": binning,
403
403
  "dataset_subsampling": nabu_config["dataset"]["projections_subsampling"],
@@ -408,7 +408,7 @@ class ProcessConfig(ProcessConfigBase):
408
408
  if nabu_config["preproc"]["flatfield"]:
409
409
  tasks.append("flatfield")
410
410
  options["flatfield"] = {
411
- # ChunkReader handles binning/subsampling by itself,
411
+ # Data reader handles binning/subsampling by itself,
412
412
  # but FlatField needs "real" indices (after binning/subsampling)
413
413
  "projs_indices": self.projs_indices(subsampling=False),
414
414
  "binning": binning,
@@ -436,6 +436,9 @@ class ProcessConfig(ProcessConfigBase):
436
436
  "flats_srcurrent": flats_srcurrent,
437
437
  }
438
438
  )
439
+ if len(dataset_info.darks) > 1:
440
+ self.logger.warning("Cannot do flat-field with more than one reduced dark. Taking the first one.")
441
+ dataset_info.darks = dataset_info.darks[sorted(dataset_info.darks.keys())[0]]
439
442
  #
440
443
  # Spikes filter
441
444
  #
@@ -460,9 +463,9 @@ class ProcessConfig(ProcessConfigBase):
460
463
  # Radios rotation (do it here if possible)
461
464
  #
462
465
  if self.get_radios_rotation_mode() == "chunk":
463
- tasks.append("rotate_projections")
464
- options["rotate_projections"] = {
465
- "angle": nabu_config["preproc"]["rotate_projections"] or dataset_info.detector_tilt,
466
+ tasks.append("tilt_correction")
467
+ options["tilt_correction"] = {
468
+ "angle": nabu_config["preproc"]["tilt_correction"] or dataset_info.detector_tilt,
466
469
  "center": nabu_config["preproc"]["rotate_projections_center"],
467
470
  "mode": "chunk",
468
471
  }
@@ -508,9 +511,9 @@ class ProcessConfig(ProcessConfigBase):
508
511
  # Radios rotation (do it here if mode=="full")
509
512
  #
510
513
  if self.get_radios_rotation_mode() == "full":
511
- tasks.append("rotate_projections")
512
- options["rotate_projections"] = {
513
- "angle": nabu_config["preproc"]["rotate_projections"] or dataset_info.detector_tilt,
514
+ tasks.append("tilt_correction")
515
+ options["tilt_correction"] = {
516
+ "angle": nabu_config["preproc"]["tilt_correction"] or dataset_info.detector_tilt,
514
517
  "center": nabu_config["preproc"]["rotate_projections_center"],
515
518
  "mode": "full",
516
519
  }
@@ -555,6 +558,7 @@ class ProcessConfig(ProcessConfigBase):
555
558
  self.rec_params,
556
559
  [
557
560
  "method",
561
+ "implementation",
558
562
  "fbp_filter_type",
559
563
  "fbp_filter_cutoff",
560
564
  "padding_type",
@@ -566,8 +570,11 @@ class ProcessConfig(ProcessConfigBase):
566
570
  "end_z",
567
571
  "centered_axis",
568
572
  "clip_outer_circle",
573
+ "outer_circle_value",
569
574
  "source_sample_dist",
570
575
  "sample_detector_dist",
576
+ "hbp_legs",
577
+ "hbp_reduction_steps",
571
578
  ],
572
579
  )
573
580
  rec_options = options["reconstruction"]
@@ -586,6 +593,8 @@ class ProcessConfig(ProcessConfigBase):
586
593
  voxel_size,
587
594
  ) # pix size is in microns in dataset_info
588
595
 
596
+ rec_options["iterations"] = nabu_config["reconstruction"]["iterations"]
597
+
589
598
  # x/y/z position information
590
599
  def get_mean_pos(position_array):
591
600
  if position_array is None:
@@ -146,7 +146,9 @@ class FullFieldReconstructor:
146
146
  else:
147
147
  self.gpu_mem = self.resources["gpus"][self._gpu_id]["memory_GB"] * self.gpu_mem_fraction
148
148
  if backend == "cuda":
149
- self._pipeline_cls = CudaChunkedPipeline
149
+ if not (__has_pycuda__):
150
+ raise RuntimeError("pycuda not avilable")
151
+ self._pipeline_cls = CudaChunkedPipeline # pylint: disable=E0606
150
152
  self.backend = backend
151
153
 
152
154
  def _compute_max_chunk_size(self):
@@ -251,7 +253,7 @@ class FullFieldReconstructor:
251
253
  if self.process_config.processing_options.get("phase", {}).get("method", None) == "CTF":
252
254
  force_grouped_mode = True
253
255
  msg = "CTF phase retrieval needs to process full radios"
254
- if self.process_config.processing_options.get("rotate_projections", {}).get("angle", 0) > 15:
256
+ if self.process_config.processing_options.get("tilt_correction", {}).get("angle", 0) > 15:
255
257
  force_grouped_mode = True
256
258
  msg = "Radios rotation with a large angle needs to process full radios"
257
259
  if self.process_config.resume_from_step == "sinogram" and force_grouped_mode:
@@ -263,7 +265,7 @@ class FullFieldReconstructor:
263
265
  self.chunk_shape = (self.n_angles, self.chunk_size, self.n_x)
264
266
  else:
265
267
  # Fall-back mode (slower)
266
- self.logger.warning(msg)
268
+ self.logger.warning(msg) # pylint: disable=E0606
267
269
  self._pipeline_mode = "grouped"
268
270
  self._compute_max_group_size()
269
271
  self.chunk_shape = (self.group_size, self.delta_z, self.n_x)
@@ -286,9 +288,10 @@ class FullFieldReconstructor:
286
288
  phase_margin = self._compute_phase_margin()
287
289
  translations_margin = self._compute_translations_margin()
288
290
  cone_margin = self._compute_cone_overlap()
291
+ rot_margin = self._compute_rotation_margin()
289
292
  # TODO radios rotation/movements
290
- margin_v = max(unsharp_margin[0], phase_margin[0], translations_margin[0], cone_margin[0])
291
- margin_h = max(unsharp_margin[1], phase_margin[1], translations_margin[1], cone_margin[1])
293
+ margin_v = max(unsharp_margin[0], phase_margin[0], translations_margin[0], cone_margin[0], rot_margin[0])
294
+ margin_h = max(unsharp_margin[1], phase_margin[1], translations_margin[1], cone_margin[1], rot_margin[1])
292
295
  if margin_v > 0:
293
296
  self.logger.info("Estimated margin: %d pixels" % margin_v)
294
297
 
@@ -360,7 +363,7 @@ class FullFieldReconstructor:
360
363
  return (max_overlap, 0)
361
364
 
362
365
  def _compute_rotation_margin(self):
363
- if "rotate_projections" in self.process_config.processing_steps:
366
+ if "tilt_correction" in self.process_config.processing_steps:
364
367
  # Partial radios rotation yields too much error in single-slice mode
365
368
  # Forcing a big margin circumvents the problem
366
369
  # This is likely to trigger the 'grouped mode', but perhaps grouped mode should always be used when rotating radios
@@ -505,8 +508,8 @@ class FullFieldReconstructor:
505
508
 
506
509
  def _print_tasks(self):
507
510
  for task in self.tasks:
508
- margin_up, margin_down = task["phase_margin"][0]
509
- s_u, s_d = task["sub_region"]
511
+ margin_up, margin_down = task["margin"][0]
512
+ s_u, s_d = task["sub_region"][1]
510
513
  print(
511
514
  "Top Margin: [%04d, %04d[ | Slices: [%04d, %04d[ | Bottom Margin: [%04d, %04d[" # pylint: disable=E1307
512
515
  % (s_u, s_u + margin_up, s_u + margin_up, s_d - margin_down, s_d - margin_down, s_d)
@@ -713,12 +716,13 @@ class FullFieldReconstructor:
713
716
  # (these values are checked in ProcessConfig._configure_resume())
714
717
  #
715
718
  patched_start_end_z = False
716
- user_rec_config = self.process_config.processing_options["reconstruction"]
717
719
  if (
718
720
  self._margin_v > 0
719
721
  and process_name != "reconstruction"
720
722
  and self.process_config.is_before_radios_cropping(process_name)
723
+ and "reconstruction" in self.process_config.processing_steps
721
724
  ):
725
+ user_rec_config = self.process_config.processing_options["reconstruction"]
722
726
  patched_start_end_z = True
723
727
  old_start_z = user_rec_config["start_z"]
724
728
  old_end_z = user_rec_config["end_z"]
@@ -1008,7 +1008,7 @@ class HelicalChunkedRegriddedPipeline:
1008
1008
  np.array((subr_start_z, subr_end_z), "i"),
1009
1009
  np.array((dtasrc_start_z, dtasrc_end_z), "i"),
1010
1010
  data_raw,
1011
- radios_angular_range_slicing # my_subsampled_indexes is important in order to compare the
1011
+ radios_angular_range_slicing, # my_subsampled_indexes is important in order to compare the
1012
1012
  # radios positions with respect to the flat position, and these position
1013
1013
  # are given as the sequential acquisition number which counts everything ( flats, darks, radios )
1014
1014
  # Insteqd, in order to access array which spans only the radios, we need to have an idea of where we are.
@@ -20,6 +20,7 @@ if __has_pycuda__:
20
20
  import pycuda.gpuarray as garray
21
21
 
22
22
 
23
+ # pylint: disable=E0606
23
24
  class CudaHelicalChunkedRegriddedPipeline(HelicalChunkedRegriddedPipeline):
24
25
  """
25
26
  Cuda backend of HelicalChunkedPipeline
@@ -468,7 +468,7 @@ class HelicalReconstructorRegridded:
468
468
  phase_margin=task["phase_margin"],
469
469
  reading_granularity=self.reading_granularity,
470
470
  span_info=self._span_info,
471
- diag_zpro_run=self.diag_zpro_run
471
+ diag_zpro_run=self.diag_zpro_run,
472
472
  # cuda_options=self.cuda_options
473
473
  )
474
474
 
nabu/pipeline/params.py CHANGED
@@ -33,7 +33,18 @@ padding_modes = {
33
33
  "zero": "zeros",
34
34
  }
35
35
 
36
- reconstruction_methods = {"fbp": "FBP", "cone": "cone", "conic": "cone", "none": None, "": None}
36
+ reconstruction_methods = {
37
+ "fbp": "FBP",
38
+ "cone": "cone",
39
+ "conic": "cone",
40
+ "none": None,
41
+ "": None,
42
+ "mlem": "mlem",
43
+ "fluo": "mlem",
44
+ "em": "mlem",
45
+ "hbp": "HBP",
46
+ "ghbp": "HBP",
47
+ }
37
48
 
38
49
  fbp_filters = {
39
50
  "ramlak": "ramlak",
@@ -64,6 +75,14 @@ optim_algorithms = {
64
75
  "fista": "fista",
65
76
  }
66
77
 
78
+ reco_implementations = {
79
+ "astra": "astra",
80
+ "corrct": "corrct",
81
+ "corr-ct": "corrct",
82
+ "nabu": "nabu",
83
+ "": None,
84
+ }
85
+
67
86
  files_formats = {
68
87
  "h5": "hdf5",
69
88
  "hdf5": "hdf5",
@@ -123,6 +142,7 @@ cor_methods = {
123
142
  "fourier-angle": "fourier-angles",
124
143
  "fourier angle": "fourier-angles",
125
144
  "octave-accurate": "octave-accurate",
145
+ "vo": "vo",
126
146
  }
127
147
 
128
148
 
@@ -168,18 +168,7 @@ class ProcessConfigBase:
168
168
 
169
169
  def _get_tilt(self):
170
170
  tilt = self.nabu_config["preproc"]["tilt_correction"]
171
- user_rot_projs = self.nabu_config["preproc"]["rotate_projections"]
172
- if user_rot_projs is not None and tilt is not None:
173
- msg = "=" * 80 + "\n"
174
- msg += (
175
- "Both 'detector_tilt' and 'rotate_projections' options were provided. The option 'rotate_projections' will take precedence. This means that the projections will be rotated by %f degrees and the option 'detector_tilt' will be ignored."
176
- % user_rot_projs
177
- )
178
- msg += "\n" + "=" * 80
179
- self.logger.warning(msg)
180
- tilt = user_rot_projs
181
- #
182
- if isinstance(tilt, str): # auto-tilt
171
+ if isinstance(tilt, str): # auto-tilt...
183
172
  self.tilt_estimator = DetectorTiltEstimator(
184
173
  self.dataset_info,
185
174
  do_flatfield=self.nabu_config["preproc"]["flatfield"],
@@ -0,0 +1,146 @@
1
+ from multiprocessing.pool import ThreadPool
2
+ import numpy as np
3
+
4
+ from nabu.utils import get_num_threads
5
+ from ..misc.binning import binning as image_binning
6
+ from ..io.reader import NXTomoReader, EDFStackReader
7
+
8
+
9
+ #
10
+ # NXTomoReader with binning
11
+ #
12
+ def bin_image_stack(src_stack, dst_stack, binning_factor=(2, 2), num_threads=8):
13
+ def _apply_binning(img_res_tuple):
14
+ img, res = img_res_tuple
15
+ res[:] = image_binning(img, binning_factor)
16
+
17
+ if dst_stack is None:
18
+ dst_stack = np.zeros((src_stack.shape[0],) + image_binning(src_stack[0], binning_factor).shape, dtype="f")
19
+
20
+ with ThreadPool(num_threads) as tp:
21
+ tp.map(_apply_binning, zip(src_stack, dst_stack))
22
+ return dst_stack
23
+
24
+
25
+ def NXTomoReaderBinning(binning_factor, *nxtomoreader_args, num_threads=None, **nxtomoreader_kwargs):
26
+ [
27
+ nxtomoreader_kwargs.pop(kwarg, None)
28
+ for kwarg in ["processing_func", "processing_func_args", "processing_func_kwargs"]
29
+ ]
30
+ nxtomoreader_kwargs["processing_func"] = bin_image_stack
31
+ nxtomoreader_kwargs["processing_func_kwargs"] = {
32
+ "binning_factor": binning_factor,
33
+ "num_threads": num_threads or get_num_threads(),
34
+ }
35
+
36
+ return NXTomoReader(
37
+ *nxtomoreader_args,
38
+ **nxtomoreader_kwargs,
39
+ )
40
+
41
+
42
+ #
43
+ # NXTomoReader with distortion correction
44
+ #
45
+
46
+
47
+ def apply_distortion_correction_on_images_stack(src_stack, dst_stack, distortion_corrector, num_threads=8):
48
+ _, subregion = distortion_corrector.get_actual_shapes_source_target()
49
+ src_x_start, src_x_end, src_z_start, src_z_end = subregion
50
+ if dst_stack is None:
51
+ dst_stack = np.zeros([src_stack.shape[0], src_z_end - src_z_start, src_x_end - src_x_start], "f")
52
+
53
+ def apply_corrector(i_img_tuple):
54
+ i, img = i_img_tuple
55
+ dst_stack[i] = distortion_corrector.transform(img)
56
+
57
+ with ThreadPool(num_threads) as tp:
58
+ tp.map(apply_corrector, enumerate(src_stack))
59
+
60
+ return dst_stack
61
+
62
+
63
+ def NXTomoReaderDistortionCorrection(distortion_corrector, *nxtomoreader_args, num_threads=None, **nxtomoreader_kwargs):
64
+ [
65
+ nxtomoreader_kwargs.pop(kwarg, None)
66
+ for kwarg in ["processing_func", "processing_func_args", "processing_func_kwargs"]
67
+ ]
68
+ nxtomoreader_kwargs["processing_func"] = apply_distortion_correction_on_images_stack
69
+ nxtomoreader_kwargs["processing_func_args"] = [distortion_corrector]
70
+ nxtomoreader_kwargs["processing_func_kwargs"] = {"num_threads": num_threads or get_num_threads()}
71
+
72
+ return NXTomoReader(
73
+ *nxtomoreader_args,
74
+ **nxtomoreader_kwargs,
75
+ )
76
+
77
+
78
+ #
79
+ # EDF Reader with binning
80
+ #
81
+
82
+
83
+ def EDFStackReaderBinning(binning_factor, *edfstackreader_args, **edfstackreader_kwargs):
84
+ [
85
+ edfstackreader_kwargs.pop(kwarg, None)
86
+ for kwarg in ["processing_func", "processing_func_args", "processing_func_kwargs"]
87
+ ]
88
+ edfstackreader_kwargs["processing_func"] = image_binning
89
+ edfstackreader_kwargs["processing_func_args"] = [binning_factor]
90
+
91
+ return EDFStackReader(
92
+ *edfstackreader_args,
93
+ **edfstackreader_kwargs,
94
+ )
95
+
96
+
97
+ #
98
+ # EDF Reader with distortion correction
99
+ #
100
+
101
+
102
+ def apply_distortion_correction_on_image(image, distortion_corrector):
103
+ return distortion_corrector.transform(image)
104
+
105
+
106
+ def EDFStackReaderDistortionCorrection(distortion_corrector, *edfstackreader_args, **edfstackreader_kwargs):
107
+ [
108
+ edfstackreader_kwargs.pop(kwarg, None)
109
+ for kwarg in ["processing_func", "processing_func_args", "processing_func_kwargs"]
110
+ ]
111
+ edfstackreader_kwargs["processing_func"] = apply_distortion_correction_on_image
112
+ edfstackreader_kwargs["processing_func_args"] = [distortion_corrector]
113
+
114
+ return EDFStackReader(
115
+ *edfstackreader_args,
116
+ **edfstackreader_kwargs,
117
+ )
118
+
119
+
120
+ def load_darks_flats(
121
+ dataset_info, sub_region, processing_func=None, processing_func_args=None, processing_func_kwargs=None
122
+ ):
123
+ """
124
+ Load the (reduced) darks and flats and crop them to the sub-region currently used.
125
+ At this stage, dataset_info.flats should be a dict in the form {num: array}
126
+
127
+ Parameters
128
+ ----------
129
+ sub_region: 2-tuple of 3-tuples of int
130
+ Tuple in the form ((start_y, end_y), (start_x, end_x))
131
+ """
132
+ (start_y, end_y), (start_x, end_x) = sub_region
133
+
134
+ processing_func_args = processing_func_args or []
135
+ processing_func_kwargs = processing_func_kwargs or {}
136
+
137
+ def proc(img):
138
+ if processing_func is None:
139
+ return img
140
+ return processing_func(img, *processing_func_args, **processing_func_kwargs)
141
+
142
+ res = {
143
+ "flats": {k: proc(flat_k)[start_y:end_y, start_x:end_x] for k, flat_k in dataset_info.flats.items()},
144
+ "darks": {k: proc(dark_k)[start_y:end_y, start_x:end_x] for k, dark_k in dataset_info.darks.items()},
145
+ }
146
+ return res
@@ -2,8 +2,8 @@ import os
2
2
  import pytest
3
3
  import numpy as np
4
4
  from nabu.testutils import utilstest, __do_long_tests__
5
- from nabu.resources.dataset_analyzer import HDF5DatasetAnalyzer
6
- from nabu.resources.dataset_analyzer import analyze_dataset
5
+ from nabu.resources.dataset_analyzer import HDF5DatasetAnalyzer, analyze_dataset
6
+ from nabu.resources.nxflatfield import update_dataset_info_flats_darks
7
7
  from nabu.resources.utils import extract_parameters
8
8
  from nabu.pipeline.estimators import CompositeCOREstimator
9
9
  from nabu.pipeline.config import parse_nabu_config_file
@@ -26,7 +26,8 @@ def bootstrap(request):
26
26
  cls.cor_pix = 1321.625
27
27
  cls.abs_tol = 0.0001
28
28
  cls.dataset_info = HDF5DatasetAnalyzer(dataset_downloaded_path)
29
- cls.cor_options = extract_parameters("""side="near"; near_pos = 300.0; near_width = 20.0 """, sep=";")
29
+ update_dataset_info_flats_darks(cls.dataset_info, True)
30
+ cls.cor_options = extract_parameters("side=300.0; near_width = 20.0", sep=";")
30
31
 
31
32
 
32
33
  @pytest.mark.skipif(not (__do_long_tests__), reason="Need NABU_LONG_TESTS=1 for this test")
@@ -52,6 +53,7 @@ def bootstrap_bamboo_reduced(request):
52
53
  conf_relpath = os.path.join("bamboo_reduced.conf")
53
54
  conf_downloaded_path = utilstest.getfile(conf_relpath)
54
55
  cls.ds_std = analyze_dataset(dataset_downloaded_path)
56
+ update_dataset_info_flats_darks(cls.ds_std, True)
55
57
  cls.conf_std = parse_nabu_config_file(conf_downloaded_path)
56
58
 
57
59
  # Dataset with estimated_cor_frm_motor
@@ -60,90 +62,60 @@ def bootstrap_bamboo_reduced(request):
60
62
  conf_relpath = os.path.join("bamboo_reduced_bliss.conf")
61
63
  conf_downloaded_path = utilstest.getfile(conf_relpath)
62
64
  cls.ds_bliss = analyze_dataset(dataset_downloaded_path)
65
+ update_dataset_info_flats_darks(cls.ds_bliss, True)
63
66
  cls.conf_bliss = parse_nabu_config_file(conf_downloaded_path)
64
67
 
65
68
 
66
69
  @pytest.mark.skipif(not (__do_long_tests__), reason="need environment variable NABU_LONG_TESTS=1")
67
70
  @pytest.mark.usefixtures("bootstrap_bamboo_reduced")
68
71
  class TestCorNearPos:
69
- true_cor = 339.486
72
+ # TODO adapt test file
73
+ true_cor = 339.486 - 0.5
70
74
 
71
75
  def test_cor_sliding_standard(self):
72
76
  cor_options = extract_parameters(self.conf_std["reconstruction"].get("cor_options", None), sep=";")
73
- finder = CORFinder("sliding-window", self.ds_std, do_flatfield=True, cor_options=cor_options)
74
- cor = finder.find_cor()
75
- message = f"Computed CoR {cor} and expected CoR {self.true_cor} do not coincide. Near_pos options was set to {cor_options.get('near_pos',None)}."
76
- assert np.isclose(self.true_cor, cor, atol=self.abs_tol), message
77
-
78
- cor_options.update({"side": "from_file"})
79
- finder = CORFinder("sliding-window", self.ds_std, do_flatfield=True, cor_options=cor_options)
80
- cor = finder.find_cor()
81
- message = f"Computed CoR {cor} and expected CoR {self.true_cor} do not coincide. Near_pos options was set to {cor_options.get('near_pos',None)}."
82
- assert np.isclose(self.true_cor, cor, atol=self.abs_tol), message
83
-
84
- cor_options.update({"side": "center"})
85
- finder = CORFinder("sliding-window", self.ds_std, do_flatfield=True, cor_options=cor_options)
86
- cor = finder.find_cor()
87
- message = f"Computed CoR {cor} and expected CoR {self.true_cor} do not coincide. Near_pos options was set to {cor_options.get('near_pos',None)}."
88
- assert np.isclose(self.true_cor, cor, atol=self.abs_tol), message
77
+ for side in [None, "from_file", "center"]:
78
+ if side is not None:
79
+ cor_options.update({"side": side})
80
+ finder = CORFinder("sliding-window", self.ds_std, do_flatfield=True, cor_options=cor_options)
81
+ cor = finder.find_cor()
82
+ message = f"Computed CoR {cor} and expected CoR {self.true_cor} do not coincide. Near_pos options was set to {cor_options.get('near_pos',None)}."
83
+ assert np.isclose(self.true_cor, cor, atol=self.abs_tol + 0.5), message # FIXME
89
84
 
90
85
  def test_cor_fourier_angles_standard(self):
91
86
  cor_options = extract_parameters(self.conf_std["reconstruction"].get("cor_options", None), sep=";")
92
- finder = SinoCORFinder("fourier-angles", self.ds_std, do_flatfield=True, cor_options=cor_options)
93
- cor = finder.find_cor()
94
- message = f"Computed CoR {cor} and expected CoR {self.true_cor} do not coincide. Near_pos options was set to {cor_options.get('near_pos',None)}."
95
- assert np.isclose(self.true_cor, cor, atol=self.abs_tol), message
96
-
97
- # Checks that it works though no data in NX
98
- cor_options.update({"side": "from_file"})
99
- finder = SinoCORFinder("fourier-angles", self.ds_std, do_flatfield=True, cor_options=cor_options)
100
- cor = finder.find_cor()
101
- message = f"Computed CoR {cor} and expected CoR {self.true_cor} do not coincide. Near_pos options was set to {cor_options.get('near_pos',None)}."
102
- assert np.isclose(self.true_cor, cor, atol=self.abs_tol), message
103
-
104
- cor_options.update({"side": "center"})
105
- finder = SinoCORFinder("fourier-angles", self.ds_std, do_flatfield=True, cor_options=cor_options)
106
- cor = finder.find_cor()
107
- message = f"Computed CoR {cor} and expected CoR {self.true_cor} do not coincide. Near_pos options was set to {cor_options.get('near_pos',None)}."
108
- assert np.isclose(self.true_cor, cor, atol=self.abs_tol), message
87
+ # TODO modify test files
88
+ if "near_pos" in cor_options and "near" in cor_options.get("side", "") == "near":
89
+ cor_options["side"] = cor_options["near_pos"]
90
+ #
91
+ for side in [None, "from_file", "center"]:
92
+ if side is not None:
93
+ cor_options.update({"side": side})
94
+ finder = SinoCORFinder("fourier-angles", self.ds_std, do_flatfield=True, cor_options=cor_options)
95
+ cor = finder.find_cor()
96
+ message = f"Computed CoR {cor} and expected CoR {self.true_cor} do not coincide. Near_pos options was set to {cor_options.get('near_pos',None)}."
97
+ assert np.isclose(self.true_cor + 0.5, cor, atol=self.abs_tol), message
109
98
 
110
99
  def test_cor_sliding_bliss(self):
111
100
  cor_options = extract_parameters(self.conf_bliss["reconstruction"].get("cor_options", None), sep=";")
112
- finder = CORFinder("sliding-window", self.ds_bliss, do_flatfield=True, cor_options=cor_options)
113
- cor = finder.find_cor()
114
- message = f"Computed CoR {cor} and expected CoR {self.true_cor} do not coincide. Near_pos options was set to {cor_options.get('near_pos',None)}."
115
- print(message)
116
- assert np.isclose(self.true_cor, cor, atol=self.abs_tol), message
117
-
118
- cor_options.update({"side": "from_file"})
119
- finder = CORFinder("sliding-window", self.ds_bliss, do_flatfield=True, cor_options=cor_options)
120
- cor = finder.find_cor()
121
- message = f"Computed CoR {cor} and expected CoR {self.true_cor} do not coincide. Near_pos options was set to {cor_options.get('near_pos',None)}."
122
- print(message)
123
- assert np.isclose(self.true_cor, cor, atol=self.abs_tol), message
124
-
125
- cor_options.update({"side": "center"})
126
- finder = CORFinder("sliding-window", self.ds_bliss, do_flatfield=True, cor_options=cor_options)
127
- cor = finder.find_cor()
128
- message = f"Computed CoR {cor} and expected CoR {self.true_cor} do not coincide. Near_pos options was set to {cor_options.get('near_pos',None)}."
129
- assert np.isclose(self.true_cor, cor, atol=self.abs_tol), message
101
+ # TODO modify test files
102
+ if "near_pos" in cor_options and "near" in cor_options.get("side", "") == "near":
103
+ cor_options["side"] = cor_options["near_pos"]
104
+ #
105
+ for side in [None, "from_file", "center"]:
106
+ if side is not None:
107
+ cor_options.update({"side": side})
108
+ finder = CORFinder("sliding-window", self.ds_bliss, do_flatfield=True, cor_options=cor_options)
109
+ cor = finder.find_cor()
110
+ message = f"Computed CoR {cor} and expected CoR {self.true_cor} do not coincide. Near_pos options was set to {cor_options.get('near_pos',None)}."
111
+ assert np.isclose(self.true_cor, cor, atol=self.abs_tol), message
130
112
 
131
113
  def test_cor_fourier_angles_bliss(self):
132
114
  cor_options = extract_parameters(self.conf_bliss["reconstruction"].get("cor_options", None), sep=";")
133
- finder = SinoCORFinder("fourier-angles", self.ds_bliss, do_flatfield=True, cor_options=cor_options)
134
- cor = finder.find_cor()
135
- message = f"Computed CoR {cor} and expected CoR {self.true_cor} do not coincide. Near_pos options was set to {cor_options.get('near_pos',None)}."
136
- assert np.isclose(self.true_cor, cor, atol=self.abs_tol), message
137
-
138
- # Checks that it works though no data in NX
139
- cor_options.update({"side": "from_file"})
140
- finder = SinoCORFinder("fourier-angles", self.ds_bliss, do_flatfield=True, cor_options=cor_options)
141
- cor = finder.find_cor()
142
- message = f"Computed CoR {cor} and expected CoR {self.true_cor} do not coincide. Near_pos options was set to {cor_options.get('near_pos',None)}."
143
- assert np.isclose(self.true_cor, cor, atol=self.abs_tol), message
144
-
145
- cor_options.update({"side": "center"})
146
- finder = SinoCORFinder("fourier-angles", self.ds_bliss, do_flatfield=True, cor_options=cor_options)
147
- cor = finder.find_cor()
148
- message = f"Computed CoR {cor} and expected CoR {self.true_cor} do not coincide. Near_pos options was set to {cor_options.get('near_pos',None)}."
149
- assert np.isclose(self.true_cor, cor, atol=self.abs_tol), message
115
+ for side in [None, "from_file", "center"]:
116
+ if side is not None:
117
+ cor_options.update({"side": side})
118
+ finder = SinoCORFinder("fourier-angles", self.ds_bliss, do_flatfield=True, cor_options=cor_options)
119
+ cor = finder.find_cor()
120
+ message = f"Computed CoR {cor} and expected CoR {self.true_cor} do not coincide. Near_pos options was set to {cor_options.get('near_pos',None)}."
121
+ assert np.isclose(self.true_cor + 0.5, cor, atol=self.abs_tol), message
nabu/pipeline/utils.py CHANGED
@@ -28,7 +28,7 @@ def pipeline_step(step_attr, step_desc):
28
28
  def decorator(func):
29
29
  def wrapper(*args, **kwargs):
30
30
  self = args[0]
31
- if self.__getattribute__(step_attr) is None:
31
+ if getattr(self, step_attr, None) is None:
32
32
  return
33
33
  self.logger.info(step_desc)
34
34
  res = func(*args, **kwargs)
@@ -38,7 +38,9 @@ def pipeline_step(step_attr, step_desc):
38
38
  for callback in callbacks:
39
39
  callback(self)
40
40
  if self.datadump_manager is not None and step_name in self.datadump_manager.data_dump:
41
- self.datadump_manager.dump_data_to_file(step_name, self.radios)
41
+ self.datadump_manager.dump_data_to_file(
42
+ step_name, self.radios, crop_margin=not (self._radios_were_cropped)
43
+ )
42
44
  return res
43
45
 
44
46
  return wrapper