nabu 2024.1.1__py3-none-any.whl → 2024.1.2__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- nabu/__init__.py +1 -1
- nabu/app/cast_volume.py +11 -2
- nabu/app/multicor.py +24 -2
- nabu/io/cast_volume.py +3 -3
- nabu/io/utils.py +2 -2
- nabu/stitching/tests/test_z_stitching.py +0 -1
- nabu/stitching/z_stitching.py +3 -3
- {nabu-2024.1.1.dist-info → nabu-2024.1.2.dist-info}/METADATA +2 -2
- nabu-2024.1.2.dist-info/RECORD +296 -0
- {nabu-2024.1.1.dist-info → nabu-2024.1.2.dist-info}/WHEEL +1 -1
- nabu-2024.1.2.dist-info/top_level.txt +2 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/doc/conf.py +0 -137
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/doc/create_conf_doc.py +0 -38
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/doc/get_mathjax.py +0 -34
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/__init__.py +0 -17
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/bootstrap.py +0 -88
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/bootstrap_stitching.py +0 -69
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/cast_volume.py +0 -272
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/cli_configs.py +0 -626
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/compare_volumes.py +0 -94
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/composite_cor.py +0 -144
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/correct_rot.py +0 -70
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/create_distortion_map_from_poly.py +0 -153
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/diag_to_pix.py +0 -358
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/diag_to_rot.py +0 -449
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/double_flatfield.py +0 -143
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/generate_header.py +0 -261
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/histogram.py +0 -197
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/multicor.py +0 -90
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/nx_z_splitter.py +0 -125
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/parse_reconstruction_log.py +0 -151
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/prepare_weights_double.py +0 -163
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/reconstruct.py +0 -120
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/reconstruct_helical.py +0 -116
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/reduce_dark_flat.py +0 -181
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/rotate.py +0 -162
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/shrink_dataset.py +0 -98
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/stitching.py +0 -85
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/tests/test_reduce_dark_flat.py +0 -78
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/utils.py +0 -33
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/validator.py +0 -110
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/__init__.py +0 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/convolution.py +0 -8
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/fft.py +0 -4
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/kernel.py +0 -97
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/medfilt.py +0 -6
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/padding.py +0 -6
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/processing.py +0 -75
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/tests/__init__.py +0 -1
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/utils.py +0 -331
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/__init__.py +0 -12
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/alignment.py +0 -578
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/cor.py +0 -1621
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/cor_sino.py +0 -183
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/distortion.py +0 -112
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/focus.py +0 -362
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/__init__.py +0 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_alignment.py +0 -70
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_cor.py +0 -472
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_focus.py +0 -105
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_tilt.py +0 -41
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_translation.py +0 -78
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tilt.py +0 -214
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/translation.py +0 -193
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/utils.py +0 -39
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/__init__.py +0 -2
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/cast_volume.py +0 -371
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/detector_distortion.py +0 -305
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/reader.py +0 -628
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/reader_helical.py +0 -114
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tests/__init__.py +0 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tests/test_cast_volume.py +0 -339
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tests/test_detector_distortion.py +0 -178
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tests/test_writers.py +0 -187
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tiffwriter_zmm.py +0 -99
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/utils.py +0 -263
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/writer.py +0 -892
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/__init__.py +0 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/binning.py +0 -98
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/fftshift.py +0 -6
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/filters.py +0 -24
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/fourier_filters.py +0 -152
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/histogram.py +0 -6
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/histogram_cuda.py +0 -8
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/kernel_base.py +0 -4
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/padding.py +0 -83
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/padding_base.py +0 -6
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/processing_base.py +0 -4
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/rotation.py +0 -6
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/rotation_cuda.py +0 -6
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/tests/__init__.py +0 -1
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/tests/test_binning.py +0 -48
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/tests/test_interpolation.py +0 -70
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/transpose.py +0 -6
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/unsharp.py +0 -4
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/unsharp_cuda.py +0 -6
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/unsharp_opencl.py +0 -8
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/utils.py +0 -117
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/__init__.py +0 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/fft.py +0 -6
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/kernel.py +0 -135
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/memcpy.py +0 -35
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/padding.py +0 -6
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/processing.py +0 -62
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/tests/__init__.py +0 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/utils.py +0 -292
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/__init__.py +0 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/config.py +0 -265
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/config_validators.py +0 -589
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/datadump.py +0 -164
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/dataset_validator.py +0 -211
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/detector_distortion_provider.py +0 -20
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/estimators.py +0 -1012
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fallback_utils.py +0 -149
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/__init__.py +0 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/chunked.py +0 -849
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/chunked_cuda.py +0 -152
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/computations.py +0 -260
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/dataset_validator.py +0 -63
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/nabu_config.py +0 -590
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/processconfig.py +0 -825
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/reconstruction.py +0 -851
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/__init__.py +0 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/dataset_validator.py +0 -19
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/fbp.py +0 -147
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/filtering.py +0 -246
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/gridded_accumulator.py +0 -575
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_chunked_regridded.py +0 -1670
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_chunked_regridded_cuda.py +0 -119
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_reconstruction.py +0 -598
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_utils.py +0 -42
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/nabu_config.py +0 -175
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/processconfig.py +0 -62
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/span_strategy.py +0 -483
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/__init__.py +0 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/test_accumulator.py +0 -157
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/test_pipeline_elements_full.py +0 -355
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/test_strategy.py +0 -61
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/utils.py +0 -51
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/weight_balancer.py +0 -101
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/params.py +0 -163
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/processconfig.py +0 -210
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/tests/test_chunk_reader.py +0 -78
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/tests/test_estimators.py +0 -149
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/utils.py +0 -116
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/writer.py +0 -193
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/xrdct/__init__.py +0 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/__init__.py +0 -7
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/alignment.py +0 -11
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ccd.py +0 -161
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ccd_cuda.py +0 -169
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ctf.py +0 -361
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ctf_cuda.py +0 -142
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/distortion.py +0 -92
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/double_flatfield.py +0 -212
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/double_flatfield_cuda.py +0 -174
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/double_flatfield_variable_region.py +0 -68
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/flatfield.py +0 -448
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/flatfield_cuda.py +0 -144
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/flatfield_variable_region.py +0 -79
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/phase.py +0 -425
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- build/lib/nabu/processing/processing_base.py +0 -123
- build/lib/nabu/processing/roll_opencl.py +0 -64
- build/lib/nabu/processing/rotation.py +0 -63
- build/lib/nabu/processing/rotation_cuda.py +0 -66
- build/lib/nabu/processing/tests/__init__.py +0 -0
- build/lib/nabu/processing/tests/test_fft.py +0 -268
- build/lib/nabu/processing/tests/test_fftshift.py +0 -71
- build/lib/nabu/processing/tests/test_histogram.py +0 -55
- build/lib/nabu/processing/tests/test_medfilt.py +0 -77
- build/lib/nabu/processing/tests/test_muladd.py +0 -54
- build/lib/nabu/processing/tests/test_padding.py +0 -247
- build/lib/nabu/processing/tests/test_roll.py +0 -63
- build/lib/nabu/processing/tests/test_rotation.py +0 -83
- build/lib/nabu/processing/tests/test_transpose.py +0 -72
- build/lib/nabu/processing/tests/test_unsharp.py +0 -106
- build/lib/nabu/processing/transpose.py +0 -126
- build/lib/nabu/processing/unsharp.py +0 -79
- build/lib/nabu/processing/unsharp_cuda.py +0 -53
- build/lib/nabu/processing/unsharp_opencl.py +0 -75
- build/lib/nabu/reconstruction/__init__.py +0 -3
- build/lib/nabu/reconstruction/cone.py +0 -241
- build/lib/nabu/reconstruction/fbp.py +0 -124
- build/lib/nabu/reconstruction/fbp_base.py +0 -391
- build/lib/nabu/reconstruction/fbp_opencl.py +0 -78
- build/lib/nabu/reconstruction/filtering.py +0 -220
- build/lib/nabu/reconstruction/filtering_cuda.py +0 -103
- build/lib/nabu/reconstruction/filtering_opencl.py +0 -111
- build/lib/nabu/reconstruction/projection.py +0 -240
- build/lib/nabu/reconstruction/reconstructor.py +0 -174
- build/lib/nabu/reconstruction/reconstructor_cuda.py +0 -44
- build/lib/nabu/reconstruction/rings.py +0 -248
- build/lib/nabu/reconstruction/rings_cuda.py +0 -322
- build/lib/nabu/reconstruction/sinogram.py +0 -467
- build/lib/nabu/reconstruction/sinogram_cuda.py +0 -250
- build/lib/nabu/reconstruction/sinogram_opencl.py +0 -40
- build/lib/nabu/reconstruction/tests/__init__.py +0 -1
- build/lib/nabu/reconstruction/tests/test_cone.py +0 -308
- build/lib/nabu/reconstruction/tests/test_deringer.py +0 -220
- build/lib/nabu/reconstruction/tests/test_fbp.py +0 -252
- build/lib/nabu/reconstruction/tests/test_filtering.py +0 -133
- build/lib/nabu/reconstruction/tests/test_halftomo.py +0 -100
- build/lib/nabu/reconstruction/tests/test_projector.py +0 -164
- build/lib/nabu/reconstruction/tests/test_reconstructor.py +0 -93
- build/lib/nabu/reconstruction/tests/test_sino_normalization.py +0 -85
- build/lib/nabu/resources/__init__.py +0 -0
- build/lib/nabu/resources/cli/__init__.py +0 -0
- build/lib/nabu/resources/cor.py +0 -5
- build/lib/nabu/resources/dataset_analyzer.py +0 -469
- build/lib/nabu/resources/gpu.py +0 -169
- build/lib/nabu/resources/logger.py +0 -130
- build/lib/nabu/resources/nxflatfield.py +0 -217
- build/lib/nabu/resources/templates/__init__.py +0 -0
- build/lib/nabu/resources/tests/__init__.py +0 -0
- build/lib/nabu/resources/tests/test_nxflatfield.py +0 -104
- build/lib/nabu/resources/tests/test_units.py +0 -47
- build/lib/nabu/resources/utils.py +0 -174
- build/lib/nabu/stitching/__init__.py +0 -0
- build/lib/nabu/stitching/alignment.py +0 -184
- build/lib/nabu/stitching/config.py +0 -1286
- build/lib/nabu/stitching/definitions.py +0 -6
- build/lib/nabu/stitching/frame_composition.py +0 -155
- build/lib/nabu/stitching/overlap.py +0 -373
- build/lib/nabu/stitching/sample_normalization.py +0 -60
- build/lib/nabu/stitching/slurm_utils.py +0 -204
- build/lib/nabu/stitching/tests/__init__.py +0 -0
- build/lib/nabu/stitching/tests/test_alignment.py +0 -99
- build/lib/nabu/stitching/tests/test_config.py +0 -226
- build/lib/nabu/stitching/tests/test_frame_composition.py +0 -180
- build/lib/nabu/stitching/tests/test_overlap.py +0 -98
- build/lib/nabu/stitching/tests/test_sample_normalization.py +0 -49
- build/lib/nabu/stitching/tests/test_slurm_utils.py +0 -146
- build/lib/nabu/stitching/tests/test_utils.py +0 -21
- build/lib/nabu/stitching/tests/test_z_stitching.py +0 -1183
- build/lib/nabu/stitching/utils.py +0 -563
- build/lib/nabu/stitching/z_stitching.py +0 -2279
- build/lib/nabu/tests.py +0 -51
- build/lib/nabu/testutils.py +0 -375
- build/lib/nabu/thirdparty/__init__.py +0 -0
- build/lib/nabu/thirdparty/algotom_convert_sino.py +0 -276
- build/lib/nabu/thirdparty/pore3d_deringer_munch.py +0 -108
- build/lib/nabu/thirdparty/tomocupy_remove_stripe.py +0 -586
- build/lib/nabu/thirdparty/tomopy_phase.py +0 -239
- build/lib/nabu/thirdparty/tomwer_load_flats_darks.py +0 -162
- build/lib/nabu/utils.py +0 -836
- nabu-2024.1.1.dist-info/RECORD +0 -2375
- nabu-2024.1.1.dist-info/top_level.txt +0 -4
- {build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app → nabu/app/tests}/__init__.py +0 -0
- {nabu-2024.1.1.dist-info → nabu-2024.1.2.dist-info}/LICENSE +0 -0
- {nabu-2024.1.1.dist-info → nabu-2024.1.2.dist-info}/entry_points.txt +0 -0
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from ...preproc.ccd_cuda import CudaLog, CudaCCDFilter
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from ...preproc.flatfield_cuda import CudaFlatFieldDataUrls
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from ...preproc.shift_cuda import CudaVerticalShift
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from ...preproc.phase_cuda import CudaPaganinPhaseRetrieval
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from ...preproc.ctf_cuda import CudaCTFPhaseRetrieval
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from ...reconstruction.sinogram_cuda import CudaSinoBuilder, CudaSinoNormalization
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from ...reconstruction.filtering_cuda import CudaSinoFilter
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from ...reconstruction.rings_cuda import CudaMunchDeringer, CudaSinoMeanDeringer, CudaVoDeringer
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from ...processing.unsharp_cuda import CudaUnsharpMask
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from ...processing.rotation_cuda import CudaRotation
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from ...processing.histogram_cuda import CudaPartialHistogram
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from ...reconstruction.fbp import Backprojector
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from ...reconstruction.cone import __have_astra__, ConebeamReconstructor
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FlatFieldClass = CudaFlatFieldDataUrls
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DoubleFlatFieldClass = CudaDoubleFlatField
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CCDCorrectionClass = CudaCCDFilter
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PaganinPhaseRetrievalClass = CudaPaganinPhaseRetrieval
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CTFPhaseRetrievalClass = CudaCTFPhaseRetrieval
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UnsharpMaskClass = CudaUnsharpMask
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ImageRotationClass = CudaRotation
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VerticalShiftClass = CudaVerticalShift
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MunchDeringerClass = CudaMunchDeringer
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SinoMeanDeringerClass = CudaSinoMeanDeringer
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VoDeringerClass = CudaVoDeringer
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MLogClass = CudaLog
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):
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d_arr = getattr(self, d_name, None)
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def _transfer_radios_to_gpu(self):
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def _process_finalize(self):
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#
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def _read_data(self):
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super()._read_data()
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self._transfer_radios_to_gpu()
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def _flatfield(self):
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super()._flatfield()
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self._transfer_radios_to_gpu()
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def _reconstruct(self):
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super()._reconstruct()
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return
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if self.processing_options["reconstruction"]["method"] == "cone":
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self.recs = self.recs.get()[U:D, ...]
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else:
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def _write_data(self, data=None):
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super()._write_data(data=data)
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if "reconstruction" in self.processing_steps:
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self.recs = self._d_recs
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self.radios = self._h_radios
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@pipeline_step("histogram", "Computing histogram")
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def _compute_histogram(self, data=None):
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if data is None:
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self.recs_histogram = self.histogram.compute_histogram(data)
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def _dump_data_to_file(self, step_name, data=None):
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if data is None:
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data = self.radios
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if step_name not in self.datadump_manager.data_dump:
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return
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if isinstance(data, garray.GPUArray):
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data = data.get()
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self.datadump_manager.dump_data_to_file(step_name, data=data)
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@@ -1,260 +0,0 @@
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from math import ceil
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from silx.image.tomography import get_next_power
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from ...utils import check_supported
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def estimate_required_memory(
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process_config, delta_z=None, delta_a=None, max_mem_allocation_GB=None, fft_plans=True, debug=False
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):
|
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"""
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Estimate the memory (RAM) in Bytes needed for a reconstruction.
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Parameters
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-----------
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process_config: `ProcessConfig` object
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Data structure with the processing configuration
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delta_z: int, optional
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How many lines are to be loaded in the each projection image.
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Default is to load lines [start_z:end_z] (where start_z and end_z come from the user configuration file)
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delta_a: int, optional
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How many (partial) projection images to load at the same time. Default is to load all the projection images.
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max_mem_allocation_GB: float, optional
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Maximum amount of memory in GB for one single array.
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|
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Returns
|
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-------
|
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required_memory: float
|
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Total required memory (in bytes).
|
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|
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Raises
|
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------
|
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ValueError if one single-array allocation exceeds "max_mem_allocation_GB"
|
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|
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Notes
|
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|
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-----
|
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pycuda <= 2022.1 cannot use arrays with more than 2**32 items (i.e 17.18 GB for float32).
|
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This was solved in more recent versions.
|
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"""
|
38
|
-
|
39
|
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def check_memory_limit(mem_GB, name):
|
40
|
-
if max_mem_allocation_GB is None:
|
41
|
-
return
|
42
|
-
if mem_GB > max_mem_allocation_GB:
|
43
|
-
raise ValueError(
|
44
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"Cannot allocate array '%s' %.3f GB > max_mem_allocation_GB = %.3f GB"
|
45
|
-
% (name, mem_GB, max_mem_allocation_GB)
|
46
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-
)
|
47
|
-
|
48
|
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dataset = process_config.dataset_info
|
49
|
-
processing_steps = process_config.processing_steps
|
50
|
-
|
51
|
-
# The "x" dimension (last axis) is always the image width, because
|
52
|
-
# - Processing is never "cut" along this axis (we either split along frames, or images lines)
|
53
|
-
# - Even if we want to reconstruct a vertical slice (i.e end_x - start_x == 1),
|
54
|
-
# the tomography reconstruction will need the full information along this axis.
|
55
|
-
# The only case where reading a x-subregion would be useful is to crop the initial data
|
56
|
-
# (i.e knowing that a part of each image will be completely unused). This is not supported yet.
|
57
|
-
Nx = process_config.radio_shape(binning=True)[-1]
|
58
|
-
|
59
|
-
if delta_z is not None:
|
60
|
-
Nz = delta_z // process_config.binning_z
|
61
|
-
else:
|
62
|
-
Nz = process_config.rec_delta_z # accounting for binning
|
63
|
-
if delta_a is not None:
|
64
|
-
Na = ceil(delta_a / process_config.subsampling_factor)
|
65
|
-
else:
|
66
|
-
Na = process_config.n_angles(subsampling=True)
|
67
|
-
|
68
|
-
total_memory_needed = 0
|
69
|
-
|
70
|
-
# Read data
|
71
|
-
# ----------
|
72
|
-
data_image_size = Nx * Nz * 4
|
73
|
-
data_volume_size = Na * data_image_size
|
74
|
-
check_memory_limit(data_volume_size / 1e9, "projections")
|
75
|
-
total_memory_needed += data_volume_size
|
76
|
-
|
77
|
-
# CCD processing
|
78
|
-
# ---------------
|
79
|
-
if "flatfield" in processing_steps:
|
80
|
-
# Flat-field is done in-place, but still need to load darks/flats
|
81
|
-
n_darks = len(dataset.darks)
|
82
|
-
n_flats = len(dataset.flats)
|
83
|
-
total_memory_needed += (n_darks + n_flats) * data_image_size
|
84
|
-
|
85
|
-
if "ccd_correction" in processing_steps:
|
86
|
-
# CCD filter is "batched 2D"
|
87
|
-
total_memory_needed += data_image_size
|
88
|
-
|
89
|
-
# Phase retrieval
|
90
|
-
# ---------------
|
91
|
-
if "phase" in processing_steps:
|
92
|
-
# Phase retrieval is done image-wise, so near in-place, but needs to allocate some memory:
|
93
|
-
# filter with padded shape, radio_padded, radio_padded_fourier, and possibly FFT plan.
|
94
|
-
# CTF phase retrieval uses "2 filters" (num and denom) but let's neglect this.
|
95
|
-
Nx_p = get_next_power(2 * Nx)
|
96
|
-
Nz_p = get_next_power(2 * Nz)
|
97
|
-
img_size_real = Nx_p * Nz_p * 4
|
98
|
-
img_size_cplx = ((Nx_p * Nz_p) // 2 + 1) * 8 # assuming RFFT
|
99
|
-
factor = 1
|
100
|
-
if fft_plans:
|
101
|
-
factor = 2
|
102
|
-
total_memory_needed += (2 * img_size_real + img_size_cplx) * factor
|
103
|
-
|
104
|
-
# Sinogram de-ringing
|
105
|
-
# -------------------
|
106
|
-
if "sino_rings_correction" in processing_steps:
|
107
|
-
method = process_config.processing_options["sino_rings_correction"]["method"]
|
108
|
-
if method == "munch":
|
109
|
-
# Process is done image-wise.
|
110
|
-
# Needs one Discrete Wavelets transform and one FFT/IFFT plan for each scale
|
111
|
-
factor = 2 if not (fft_plans) else 5.5 # approx!
|
112
|
-
total_memory_needed += (Nx * Na * 4) * factor
|
113
|
-
elif method == "vo":
|
114
|
-
# cupy-based implementation makes many calls to "scipy-like" functions, where the memory usage is not under control
|
115
|
-
# TODO try to estimate this
|
116
|
-
pass
|
117
|
-
|
118
|
-
# Reconstruction
|
119
|
-
# ---------------
|
120
|
-
reconstructed_volume_size = 0
|
121
|
-
if "reconstruction" in processing_steps:
|
122
|
-
rec_config = process_config.processing_options["reconstruction"]
|
123
|
-
Nx_rec = rec_config["end_x"] - rec_config["start_x"] + 1
|
124
|
-
Ny_rec = rec_config["end_y"] - rec_config["start_y"] + 1
|
125
|
-
reconstructed_volume_size = Nz * Nx_rec * Ny_rec * 4
|
126
|
-
check_memory_limit(reconstructed_volume_size / 1e9, "reconstructions")
|
127
|
-
total_memory_needed += reconstructed_volume_size
|
128
|
-
if process_config.rec_params["method"] == "cone":
|
129
|
-
# In cone-beam reconstruction, need both sinograms and reconstruction inside GPU.
|
130
|
-
# That's big!
|
131
|
-
total_memory_needed += 2 * data_volume_size
|
132
|
-
|
133
|
-
if debug:
|
134
|
-
print(
|
135
|
-
"Mem for (delta_z=%s, delta_a=%s) ==> (Na=%d, Nz=%d, Nx=%d) : %.3f GB"
|
136
|
-
% (delta_z, delta_a, Na, Nz, Nx, total_memory_needed / 1e9)
|
137
|
-
)
|
138
|
-
|
139
|
-
return total_memory_needed
|
140
|
-
|
141
|
-
|
142
|
-
def estimate_max_chunk_size(
|
143
|
-
available_memory_GB,
|
144
|
-
process_config,
|
145
|
-
pipeline_part="all",
|
146
|
-
n_rows=None,
|
147
|
-
step=10,
|
148
|
-
max_mem_allocation_GB=None,
|
149
|
-
fft_plans=True,
|
150
|
-
debug=False,
|
151
|
-
):
|
152
|
-
"""
|
153
|
-
Estimate the maximum size of the data chunk that can be loaded in memory.
|
154
|
-
|
155
|
-
Parameters
|
156
|
-
----------
|
157
|
-
available_memory_GB: float
|
158
|
-
available memory in Giga Bytes (GB - not GiB !).
|
159
|
-
process_config: ProcessConfig
|
160
|
-
ProcessConfig object
|
161
|
-
pipeline_part: str
|
162
|
-
Which pipeline part to consider. Possible options are:
|
163
|
-
- "full": Account for all the pipeline steps (reading data all the way to reconstruction).
|
164
|
-
- "radios": Consider only the processing steps on projection images (ignore sinogram-based steps and reconstruction)
|
165
|
-
- "sinogram": Consider only the processing steps related to sinograms and reconstruction
|
166
|
-
n_rows: int, optional
|
167
|
-
How many lines to load in each projection. Only accounted for pipeline_part="radios".
|
168
|
-
step: int, optional
|
169
|
-
Step size when doing the iterative memory estimation
|
170
|
-
max_mem_allocation_GB: float, optional
|
171
|
-
Maximum size (in GB) for one single array.
|
172
|
-
|
173
|
-
Returns
|
174
|
-
-------
|
175
|
-
n_max: int
|
176
|
-
If pipeline_par is "full" or "sinos": return the maximum number of lines that can be loaded
|
177
|
-
in all the projections while fitting memory, i.e `data[:, 0:n_max, :]`
|
178
|
-
If pipeline_part is "radios", return the maximum number of (partial) images that can be loaded
|
179
|
-
while fitting memory, i.e `data[:, zmin:zmax, 0:n_max]`
|
180
|
-
|
181
|
-
|
182
|
-
Notes
|
183
|
-
-----
|
184
|
-
pycuda <= 2022.1 cannot use arrays with more than 2**32 items (i.e 17.18 GB for float32).
|
185
|
-
This was solved in more recent versions.
|
186
|
-
"""
|
187
|
-
|
188
|
-
supported_pipeline_parts = ["all", "radios", "sinos"]
|
189
|
-
check_supported(pipeline_part, supported_pipeline_parts, "pipeline_part")
|
190
|
-
|
191
|
-
processing_steps_bak = process_config.processing_steps.copy()
|
192
|
-
reconstruction_steps = ["sino_rings_correction", "reconstruction"]
|
193
|
-
|
194
|
-
if pipeline_part == "all":
|
195
|
-
# load lines from all the projections
|
196
|
-
delta_a = None
|
197
|
-
delta_z = 0
|
198
|
-
if pipeline_part == "radios":
|
199
|
-
# order should not matter
|
200
|
-
process_config.processing_steps = list(set(process_config.processing_steps) - set(reconstruction_steps))
|
201
|
-
# load lines from only a subset of projections
|
202
|
-
delta_a = 0
|
203
|
-
delta_z = n_rows
|
204
|
-
if pipeline_part == "sinos":
|
205
|
-
process_config.processing_steps = [
|
206
|
-
step for step in process_config.processing_steps if step in reconstruction_steps
|
207
|
-
]
|
208
|
-
# load lines from all the projections
|
209
|
-
delta_a = None
|
210
|
-
delta_z = 0
|
211
|
-
|
212
|
-
mem = 0
|
213
|
-
last_valid_delta_a = delta_a
|
214
|
-
last_valid_delta_z = delta_z
|
215
|
-
while True:
|
216
|
-
try:
|
217
|
-
mem = estimate_required_memory(
|
218
|
-
process_config,
|
219
|
-
delta_z=delta_z,
|
220
|
-
delta_a=delta_a,
|
221
|
-
max_mem_allocation_GB=max_mem_allocation_GB,
|
222
|
-
fft_plans=fft_plans,
|
223
|
-
debug=debug,
|
224
|
-
)
|
225
|
-
except ValueError:
|
226
|
-
# For very big dataset this function might return "0".
|
227
|
-
# Either start at 1, or use a smaller step...
|
228
|
-
break
|
229
|
-
if mem / 1e9 > available_memory_GB:
|
230
|
-
break
|
231
|
-
if delta_a is not None and delta_a > process_config.n_angles():
|
232
|
-
break
|
233
|
-
if delta_z is not None and delta_z > process_config.radio_shape()[0]:
|
234
|
-
break
|
235
|
-
last_valid_delta_a, last_valid_delta_z = delta_a, delta_z
|
236
|
-
if pipeline_part == "radios":
|
237
|
-
delta_a += step
|
238
|
-
else:
|
239
|
-
delta_z += step
|
240
|
-
|
241
|
-
process_config.processing_steps = processing_steps_bak
|
242
|
-
|
243
|
-
if pipeline_part != "radios":
|
244
|
-
if mem / 1e9 < available_memory_GB:
|
245
|
-
res = min(delta_z, process_config.radio_shape()[0])
|
246
|
-
else:
|
247
|
-
res = last_valid_delta_z
|
248
|
-
else:
|
249
|
-
if mem / 1e9 < available_memory_GB:
|
250
|
-
res = min(delta_a, process_config.n_angles())
|
251
|
-
else:
|
252
|
-
res = last_valid_delta_a
|
253
|
-
|
254
|
-
# Really not ideal. For very large dataset, "step" should be very small.
|
255
|
-
# Otherwise we go from 0 -> OK to 10 -> not OK, and then retain 0...
|
256
|
-
if res == 0:
|
257
|
-
res = 1
|
258
|
-
#
|
259
|
-
|
260
|
-
return res
|
@@ -1,63 +0,0 @@
|
|
1
|
-
import os
|
2
|
-
from ..dataset_validator import DatasetValidatorBase
|
3
|
-
|
4
|
-
|
5
|
-
class FullFieldDatasetValidator(DatasetValidatorBase):
|
6
|
-
def _validate(self):
|
7
|
-
self._check_not_empty()
|
8
|
-
self._convert_negative_indices()
|
9
|
-
self._get_output_filename()
|
10
|
-
self._check_can_do_flatfield()
|
11
|
-
self._check_can_do_phase()
|
12
|
-
self._check_can_do_reconstruction()
|
13
|
-
self._check_slice_indices()
|
14
|
-
self._handle_processing_mode()
|
15
|
-
self._handle_binning()
|
16
|
-
self._check_output_file()
|
17
|
-
|
18
|
-
def _check_can_do_flatfield(self):
|
19
|
-
if self.nabu_config["preproc"]["flatfield"]:
|
20
|
-
darks = self.dataset_info.darks
|
21
|
-
assert len(darks) > 0, "Need at least one dark to perform flat-field correction"
|
22
|
-
for dark_id, dark_url in darks.items():
|
23
|
-
assert os.path.isfile(dark_url.file_path()), "Dark file %s not found" % dark_url.file_path()
|
24
|
-
flats = self.dataset_info.flats
|
25
|
-
assert len(flats) > 0, "Need at least one flat to perform flat-field correction"
|
26
|
-
for flat_id, flat_url in flats.items():
|
27
|
-
assert os.path.isfile(flat_url.file_path()), "Flat file %s not found" % flat_url.file_path()
|
28
|
-
|
29
|
-
def _check_slice_indices(self):
|
30
|
-
nx, nz = self.dataset_info.radio_dims
|
31
|
-
rec_params = self.rec_params
|
32
|
-
if rec_params["enable_halftomo"]:
|
33
|
-
ny, nx = self._get_nx_ny()
|
34
|
-
what = (("start_x", "end_x", nx), ("start_y", "end_y", nx), ("start_z", "end_z", nz))
|
35
|
-
for start_name, end_name, numels in what:
|
36
|
-
self._check_start_end_idx(
|
37
|
-
rec_params[start_name], rec_params[end_name], numels, start_name=start_name, end_name=end_name
|
38
|
-
)
|
39
|
-
|
40
|
-
def _check_can_do_phase(self):
|
41
|
-
if self.nabu_config["phase"]["method"] is None:
|
42
|
-
return
|
43
|
-
self.dataset_info.check_defined_attribute("distance")
|
44
|
-
self.dataset_info.check_defined_attribute("pixel_size")
|
45
|
-
|
46
|
-
def _check_can_do_reconstruction(self):
|
47
|
-
rec_options = self.nabu_config["reconstruction"]
|
48
|
-
if rec_options["method"] is None:
|
49
|
-
return
|
50
|
-
self.dataset_info.check_defined_attribute("pixel_size")
|
51
|
-
if rec_options["method"] == "cone":
|
52
|
-
if rec_options["source_sample_dist"] is None:
|
53
|
-
err_msg = "In cone-beam reconstruction, you have to provide 'source_sample_dist' in [reconstruction]"
|
54
|
-
self.logger.fatal(err_msg)
|
55
|
-
raise ValueError(err_msg)
|
56
|
-
if rec_options["sample_detector_dist"] is None:
|
57
|
-
if self.dataset_info.distance is None:
|
58
|
-
err_msg = "Cone-beam reconstruction: 'sample_detector_dist' was not provided but could not be found in the dataset metadata either. Please provide 'sample_detector_dist'"
|
59
|
-
self.logger.fatal(err_msg)
|
60
|
-
raise ValueError(err_msg)
|
61
|
-
self.logger.warning(
|
62
|
-
"Cone-beam reconstruction: 'sample_detector_dist' not provided, will use the one in dataset metadata"
|
63
|
-
)
|