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/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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Utility to convert the "Lmicron" parameter of PyHST
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Energy in keV.
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Paganin Phase Retrieval for an infinitely distant point source.
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refractive index of the sample.
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the padding of the parts related to the zero values will
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fall back to the one of "padding" parameter.
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For example, if padding="edge" and L, R are 0, then
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the left and right parts will be padded with the edges, while
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the Up and Down parts will be padded using the the user-provided
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margins of the radio, and the final data will have shape
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(Nrows - U - D, Ncols).
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Some or all the values U, D, L, R can be the string "auto".
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In this case, the values of U, D, L, R are automatically computed
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as a function of the Paganin filter width.
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use_rfft: bool, optional
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Whether to use Real-to-Complex (R2C) transform instead of
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standard Complex-to-Complex transform, providing better performances
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use_R2C: bool, optional
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DEPRECATED, use use_rfft instead
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fftw_num_threads: bool or None or int, optional
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DEPRECATED - please use fft_num_threads
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fft_num_threads: bool or None or int, optional
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Number of threads for FFT.
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Default is to use all available threads. You can pass a negative number
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to use N - fft_num_threads cores.
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Important
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----------
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Mind the units! Distance and pixel size are in meters, and energy is in keV.
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-
|
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-
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Notes
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------
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-
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**Padding methods**
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The phase retrieval is a convolution done in Fourier domain using FFT,
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so the Fourier transform size has to be at least twice the size of
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the original data. Mathematically, the data should be padded with zeros
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before being Fourier transformed. However, in practice, this can lead
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to artefacts at the edges (Gibbs effect) if the data does not go to
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zero at the edges.
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Apart from applying an apodization (Hamming, Blackman, etc), a common
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strategy to avoid these artefacts is to pad the data.
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In tomography reconstruction, this is usually done by replicating the
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last(s) value(s) of the edges ; but one can think of other methods:
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|
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- "zeros": the data is simply padded with zeros.
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- "mean": the upper side of extended data is padded with the mean of
|
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the first row, the lower side with the mean of the last row, etc.
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- "edge": the data is padded by replicating the edges.
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This is the default mode.
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- "sym": the data is padded by mirroring the data with respect
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to its edges. See ``numpy.pad()``.
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- "reflect": the data is padded by reflecting the data with respect
|
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to its edges, including the edges. See ``numpy.pad()``.
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**Formulas**
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The radio is divided, in the Fourier domain, by the original "Paganin filter" `[1]`.
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|
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.. math::
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|
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F = 1 + \\frac{\\delta}{\\beta} \\lambda D \\pi |k|^2
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-
|
164
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where k is the wave vector.
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References
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-----------
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[1] D. Paganin Et Al, "Simultaneous phase and amplitude extraction
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from a single defocused image of a homogeneous object",
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Journal of Microscopy, Vol 206, Part 1, 2002
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"""
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self._init_parameters(distance, energy, pixel_size, delta_beta, padding)
|
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self._calc_shape(shape, margin)
|
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# COMPAT.
|
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if use_R2C is not None:
|
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deprecation_warning("'use_R2C' is replaced with 'use_rfft'", func_name="pag_r2c")
|
178
|
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if fftw_num_threads is not None:
|
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|
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deprecation_warning("'fftw_num_threads' is replaced with 'fft_num_threads'", func_name="pag_fftw")
|
180
|
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fft_num_threads = fftw_num_threads
|
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|
-
# ---
|
182
|
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self._get_fft(use_rfft, fft_num_threads)
|
183
|
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self.compute_filter()
|
184
|
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|
185
|
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def _init_parameters(self, distance, energy, pixel_size, delta_beta, padding):
|
186
|
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self.distance_cm = distance * 1e2
|
187
|
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self.distance_micron = distance * 1e6
|
188
|
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self.energy_kev = energy
|
189
|
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self.pixel_size_micron = pixel_size * 1e6
|
190
|
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self.delta_beta = delta_beta
|
191
|
-
self.wavelength_micron = 1.23984199e-3 / self.energy_kev
|
192
|
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self.padding = padding
|
193
|
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self.padding_methods = {
|
194
|
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"zeros": self._pad_zeros,
|
195
|
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"mean": self._pad_mean,
|
196
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"edge": self._pad_edge,
|
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"symmetric": self._pad_sym,
|
198
|
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"reflect": self._pad_reflect,
|
199
|
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}
|
200
|
-
|
201
|
-
def _get_fft(self, use_rfft, fft_num_threads):
|
202
|
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self.use_rfft = use_rfft
|
203
|
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self.use_R2C = use_rfft # Compat.
|
204
|
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self.fft_num_threads = get_num_threads(fft_num_threads)
|
205
|
-
if self.use_rfft:
|
206
|
-
self.fft_func = rfft2
|
207
|
-
self.ifft_func = irfft2
|
208
|
-
else:
|
209
|
-
self.fft_func = fft2
|
210
|
-
self.ifft_func = ifft2
|
211
|
-
|
212
|
-
def _calc_shape(self, shape, margin):
|
213
|
-
if np.isscalar(shape):
|
214
|
-
shape = (shape, shape)
|
215
|
-
else:
|
216
|
-
assert len(shape) == 2
|
217
|
-
self.shape = shape
|
218
|
-
self._set_margin_value(margin)
|
219
|
-
self._calc_padded_shape()
|
220
|
-
|
221
|
-
def _set_margin_value(self, margin):
|
222
|
-
self.margin = margin
|
223
|
-
if margin is None:
|
224
|
-
self.shape_inner = self.shape
|
225
|
-
self.use_margin = False
|
226
|
-
self.margin = ((0, 0), (0, 0))
|
227
|
-
return
|
228
|
-
self.use_margin = True
|
229
|
-
try:
|
230
|
-
((U, D), (L, R)) = margin
|
231
|
-
except ValueError:
|
232
|
-
raise ValueError("Expected margin in the format ((U, D), (L, R))")
|
233
|
-
for val in [U, D, L, R]:
|
234
|
-
if isinstance(val, str) and val != "auto":
|
235
|
-
raise ValueError("Expected either an integer, or 'auto'")
|
236
|
-
if int(val) != val or val < 0:
|
237
|
-
raise ValueError("Expected positive integers for margin values")
|
238
|
-
self.shape_inner = (self.shape[0] - U - D, self.shape[1] - L - R)
|
239
|
-
|
240
|
-
def _calc_padded_shape(self):
|
241
|
-
"""
|
242
|
-
Compute the padded shape.
|
243
|
-
If margin = 0, length_padded = next_power(2*length).
|
244
|
-
Otherwise : length_padded = next_power(2*(length - margins))
|
245
|
-
|
246
|
-
Principle
|
247
|
-
----------
|
248
|
-
|
249
|
-
<--------------------- nx_p --------------------->
|
250
|
-
| | original data | |
|
251
|
-
< -- Pl - ><-- L -->< -- nx --><-- R --><-- Pr -->
|
252
|
-
<----------- nx0 ----------->
|
253
|
-
|
254
|
-
Pl, Pr : left/right padding length
|
255
|
-
L, R : left/right margin
|
256
|
-
nx : length of inner data (and length of final result)
|
257
|
-
nx0 : length of original data
|
258
|
-
nx_p : total length of padded data
|
259
|
-
"""
|
260
|
-
n_y, n_x = self.shape_inner
|
261
|
-
n_y0, n_x0 = self.shape
|
262
|
-
n_y_p = self._get_next_power(max(2 * n_y, n_y0))
|
263
|
-
n_x_p = self._get_next_power(max(2 * n_x, n_x0))
|
264
|
-
self.shape_padded = (n_y_p, n_x_p)
|
265
|
-
self.data_padded = np.zeros((n_y_p, n_x_p), dtype=np.float64)
|
266
|
-
|
267
|
-
((U, D), (L, R)) = self.margin
|
268
|
-
n_y0, n_x0 = self.shape
|
269
|
-
self.pad_top_len = (n_y_p - n_y0) // 2
|
270
|
-
self.pad_bottom_len = n_y_p - n_y0 - self.pad_top_len
|
271
|
-
self.pad_left_len = (n_x_p - n_x0) // 2
|
272
|
-
self.pad_right_len = n_x_p - n_x0 - self.pad_left_len
|
273
|
-
|
274
|
-
def _get_next_power(self, n):
|
275
|
-
"""
|
276
|
-
Given a number, get the closest (upper) number p such that
|
277
|
-
p is a power of 2, 3, 5 and 7.
|
278
|
-
"""
|
279
|
-
idx = bisect(self.powers, n)
|
280
|
-
if self.powers[idx - 1] == n:
|
281
|
-
return n
|
282
|
-
return self.powers[idx]
|
283
|
-
|
284
|
-
def compute_filter(self):
|
285
|
-
nyp, nxp = self.shape_padded
|
286
|
-
fftfreq = np.fft.rfftfreq if self.use_rfft else np.fft.fftfreq
|
287
|
-
fy = np.fft.fftfreq(nyp, d=self.pixel_size_micron)
|
288
|
-
fx = fftfreq(nxp, d=self.pixel_size_micron)
|
289
|
-
self._coords_grid = np.add.outer(fy**2, fx**2)
|
290
|
-
#
|
291
|
-
k2 = self._coords_grid
|
292
|
-
D = self.distance_micron
|
293
|
-
L = self.wavelength_micron
|
294
|
-
db = self.delta_beta
|
295
|
-
self.paganin_filter = 1.0 / (1 + db * L * D * pi * k2)
|
296
|
-
|
297
|
-
def pad_with_values(self, data, top_val=0, bottom_val=0, left_val=0, right_val=0):
|
298
|
-
"""
|
299
|
-
Pad the data into `self.padded_data` with values.
|
300
|
-
|
301
|
-
Parameters
|
302
|
-
----------
|
303
|
-
data: numpy.ndarray
|
304
|
-
data (radio)
|
305
|
-
top_val: float or numpy.ndarray, optional
|
306
|
-
Value(s) to fill the top of the padded data with.
|
307
|
-
bottom_val: float or numpy.ndarray, optional
|
308
|
-
Value(s) to fill the bottom of the padded data with.
|
309
|
-
left_val: float or numpy.ndarray, optional
|
310
|
-
Value(s) to fill the left of the padded data with.
|
311
|
-
right_val: float or numpy.ndarray, optional
|
312
|
-
Value(s) to fill the right of the padded data with.
|
313
|
-
"""
|
314
|
-
self.data_padded.fill(0)
|
315
|
-
Pu, Pd = self.pad_top_len, self.pad_bottom_len
|
316
|
-
Pl, Pr = self.pad_left_len, self.pad_right_len
|
317
|
-
self.data_padded[:Pu, :] = top_val
|
318
|
-
self.data_padded[-Pd:, :] = bottom_val
|
319
|
-
self.data_padded[:, :Pl] = left_val
|
320
|
-
self.data_padded[:, -Pr:] = right_val
|
321
|
-
self.data_padded[Pu:-Pd, Pl:-Pr] = data
|
322
|
-
# Transform the data to the FFT layout
|
323
|
-
self.data_padded = np.roll(self.data_padded, (-Pu, -Pl), axis=(0, 1))
|
324
|
-
|
325
|
-
def _pad_zeros(self, data):
|
326
|
-
return self.pad_with_values(data, top_val=0, bottom_val=0, left_val=0, right_val=0)
|
327
|
-
|
328
|
-
def _pad_mean(self, data):
|
329
|
-
"""
|
330
|
-
Pad the data at each border with a different constant value.
|
331
|
-
The value depends on the padding size:
|
332
|
-
- On the left, value = mean(first data column)
|
333
|
-
- On the right, value = mean(last data column)
|
334
|
-
- On the top, value = mean(first data row)
|
335
|
-
- On the bottom, value = mean(last data row)
|
336
|
-
"""
|
337
|
-
return self.pad_with_values(
|
338
|
-
data,
|
339
|
-
top_val=np.mean(data[0, :]),
|
340
|
-
bottom_val=np.mean(data[-1, :]),
|
341
|
-
left_val=np.mean(data[:, 0]),
|
342
|
-
right_val=np.mean(data[:, -1]),
|
343
|
-
)
|
344
|
-
|
345
|
-
def _pad_numpy(self, data, mode):
|
346
|
-
data_padded = np.pad(
|
347
|
-
data, ((self.pad_top_len, self.pad_bottom_len), (self.pad_left_len, self.pad_right_len)), mode=mode
|
348
|
-
)
|
349
|
-
# Transform the data to the FFT layout
|
350
|
-
Pu, Pl = self.pad_top_len, self.pad_left_len
|
351
|
-
return np.roll(data_padded, (-Pu, -Pl), axis=(0, 1))
|
352
|
-
|
353
|
-
def _pad_edge(self, data):
|
354
|
-
self.data_padded = self._pad_numpy(data, mode="edge")
|
355
|
-
|
356
|
-
def _pad_sym(self, data):
|
357
|
-
self.data_padded = self._pad_numpy(data, mode="symmetric")
|
358
|
-
|
359
|
-
def _pad_reflect(self, data):
|
360
|
-
self.data_padded = self._pad_numpy(data, mode="reflect")
|
361
|
-
|
362
|
-
def pad_data(self, data, padding_method=None):
|
363
|
-
padding_method = padding_method or self.padding
|
364
|
-
check_supported(padding_method, self.available_padding_modes, "padding mode")
|
365
|
-
if padding_method not in self.padding_methods:
|
366
|
-
raise ValueError(
|
367
|
-
"Unknown padding method %s. Available are: %s"
|
368
|
-
% (padding_method, str(list(self.padding_methods.keys())))
|
369
|
-
)
|
370
|
-
pad_func = self.padding_methods[padding_method]
|
371
|
-
pad_func(data)
|
372
|
-
return self.data_padded
|
373
|
-
|
374
|
-
def apply_filter(self, radio, padding_method=None, output=None):
|
375
|
-
self.pad_data(radio, padding_method=padding_method)
|
376
|
-
radio_f = self.fft_func(self.data_padded, workers=self.fft_num_threads)
|
377
|
-
radio_f *= self.paganin_filter
|
378
|
-
radio_filtered = self.ifft_func(radio_f, workers=self.fft_num_threads).real
|
379
|
-
s0, s1 = self.shape_inner
|
380
|
-
((U, _), (L, _)) = self.margin
|
381
|
-
if output is None:
|
382
|
-
return radio_filtered[U : U + s0, L : L + s1]
|
383
|
-
else:
|
384
|
-
output[:, :] = radio_filtered[U : U + s0, L : L + s1]
|
385
|
-
return output
|
386
|
-
|
387
|
-
def lmicron_to_db(self, Lmicron):
|
388
|
-
"""
|
389
|
-
Utility to convert the "Lmicron" parameter of PyHST
|
390
|
-
to a value of delta/beta.
|
391
|
-
Please see the doc of nabu.preproc.phase.lmicron_to_db()
|
392
|
-
"""
|
393
|
-
return lmicron_to_db(Lmicron, self.energy_kev, self.distance_micron)
|
394
|
-
|
395
|
-
__call__ = apply_filter
|
396
|
-
|
397
|
-
retrieve_phase = apply_filter
|
398
|
-
|
399
|
-
|
400
|
-
def compute_paganin_margin(shape, cutoff=1e3, **pag_kwargs):
|
401
|
-
"""
|
402
|
-
Compute the convolution margin to use when calling PaganinPhaseRetrieval class.
|
403
|
-
|
404
|
-
Parameters
|
405
|
-
-----------
|
406
|
-
shape: tuple
|
407
|
-
Detector shape in the form (n_z, n_x)
|
408
|
-
"""
|
409
|
-
P = PaganinPhaseRetrieval(shape, **pag_kwargs)
|
410
|
-
|
411
|
-
ifft_func = np.fft.irfft2 if P.use_rfft else np.fft.ifft2
|
412
|
-
conv_kernel = ifft_func(P.paganin_filter)
|
413
|
-
|
414
|
-
vmax = conv_kernel[0, 0]
|
415
|
-
|
416
|
-
v_margin = get_decay(conv_kernel[:, 0], cutoff=cutoff, vmax=vmax)
|
417
|
-
h_margin = get_decay(conv_kernel[0, :], cutoff=cutoff, vmax=vmax)
|
418
|
-
# If the Paganin filter is very narrow, then the corresponding convolution
|
419
|
-
# kernel is constant, and np.argmax() gives 0 (when it should give the max value)
|
420
|
-
if v_margin == 0:
|
421
|
-
v_margin = shape[0]
|
422
|
-
if h_margin == 0:
|
423
|
-
h_margin = shape[1]
|
424
|
-
|
425
|
-
return v_margin, h_margin
|
@@ -1,143 +0,0 @@
|
|
1
|
-
import numpy as np
|
2
|
-
import pycuda.driver as cuda
|
3
|
-
from ..utils import get_cuda_srcfile, check_supported, docstring
|
4
|
-
from ..cuda.processing import CudaProcessing
|
5
|
-
from ..processing.fft_cuda import get_fft_class
|
6
|
-
from .phase import PaganinPhaseRetrieval
|
7
|
-
|
8
|
-
|
9
|
-
class CudaPaganinPhaseRetrieval(PaganinPhaseRetrieval):
|
10
|
-
supported_paddings = ["zeros", "constant", "edge"]
|
11
|
-
|
12
|
-
@docstring(PaganinPhaseRetrieval)
|
13
|
-
def __init__(
|
14
|
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self,
|
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|
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shape,
|
16
|
-
distance=0.5,
|
17
|
-
energy=20,
|
18
|
-
delta_beta=250.0,
|
19
|
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pixel_size=1e-6,
|
20
|
-
padding="edge",
|
21
|
-
margin=None,
|
22
|
-
cuda_options=None,
|
23
|
-
fftw_num_threads=None, # COMPAT.
|
24
|
-
fft_num_threads=None,
|
25
|
-
fft_backend="skcuda",
|
26
|
-
):
|
27
|
-
"""
|
28
|
-
Please refer to the documentation of
|
29
|
-
nabu.preproc.phase.PaganinPhaseRetrieval
|
30
|
-
"""
|
31
|
-
padding = self._check_padding(padding)
|
32
|
-
self.cuda_processing = CudaProcessing(**(cuda_options or {}))
|
33
|
-
super().__init__(
|
34
|
-
shape,
|
35
|
-
distance=distance,
|
36
|
-
energy=energy,
|
37
|
-
delta_beta=delta_beta,
|
38
|
-
pixel_size=pixel_size,
|
39
|
-
padding=padding,
|
40
|
-
margin=margin,
|
41
|
-
use_rfft=True,
|
42
|
-
fft_num_threads=False,
|
43
|
-
)
|
44
|
-
self._init_gpu_arrays()
|
45
|
-
self._init_fft(fft_backend)
|
46
|
-
self._init_padding_kernel()
|
47
|
-
self._init_mult_kernel()
|
48
|
-
|
49
|
-
def _check_padding(self, padding):
|
50
|
-
check_supported(padding, self.supported_paddings, "padding")
|
51
|
-
if padding == "zeros":
|
52
|
-
padding = "constant"
|
53
|
-
return padding
|
54
|
-
|
55
|
-
def _init_gpu_arrays(self):
|
56
|
-
self.d_paganin_filter = self.cuda_processing.to_device(
|
57
|
-
"d_paganin_filter", np.ascontiguousarray(self.paganin_filter, dtype=np.float32)
|
58
|
-
)
|
59
|
-
|
60
|
-
# overwrite parent method, don't initialize any FFT plan
|
61
|
-
def _get_fft(self, use_rfft, fft_num_threads):
|
62
|
-
self.use_rfft = use_rfft
|
63
|
-
|
64
|
-
def _init_fft(self, fft_backend):
|
65
|
-
fft_cls = get_fft_class(backend=fft_backend)
|
66
|
-
self.cufft = fft_cls(shape=self.data_padded.shape, dtype=np.float32, r2c=True)
|
67
|
-
self.d_radio_padded = self.cuda_processing.allocate_array("d_radio_padded", self.cufft.shape, "f")
|
68
|
-
self.d_radio_f = self.cuda_processing.allocate_array("d_radio_f", self.cufft.shape_out, np.complex64)
|
69
|
-
|
70
|
-
def _init_padding_kernel(self):
|
71
|
-
kern_signature = {"constant": "Piiiiiiiiffff", "edge": "Piiiiiiii"}
|
72
|
-
self.padding_kernel = self.cuda_processing.kernel(
|
73
|
-
"padding_%s" % self.padding,
|
74
|
-
filename=get_cuda_srcfile("padding.cu"),
|
75
|
-
signature=kern_signature[self.padding],
|
76
|
-
)
|
77
|
-
Ny, Nx = self.shape
|
78
|
-
Nyp, Nxp = self.shape_padded
|
79
|
-
self.padding_kernel_args = [
|
80
|
-
self.d_radio_padded,
|
81
|
-
Nx,
|
82
|
-
Ny,
|
83
|
-
Nxp,
|
84
|
-
Nyp,
|
85
|
-
self.pad_left_len,
|
86
|
-
self.pad_right_len,
|
87
|
-
self.pad_top_len,
|
88
|
-
self.pad_bottom_len,
|
89
|
-
]
|
90
|
-
# TODO configurable constant values
|
91
|
-
if self.padding == "constant":
|
92
|
-
self.padding_kernel_args.extend([0, 0, 0, 0])
|
93
|
-
|
94
|
-
def _init_mult_kernel(self):
|
95
|
-
self.cpxmult_kernel = self.cuda_processing.kernel(
|
96
|
-
"inplace_complexreal_mul_2Dby2D",
|
97
|
-
filename=get_cuda_srcfile("ElementOp.cu"),
|
98
|
-
signature="PPii",
|
99
|
-
)
|
100
|
-
self.cpxmult_kernel_args = [
|
101
|
-
self.d_radio_f,
|
102
|
-
self.d_paganin_filter,
|
103
|
-
self.shape_padded[1] // 2 + 1,
|
104
|
-
self.shape_padded[0],
|
105
|
-
]
|
106
|
-
|
107
|
-
def set_input(self, data):
|
108
|
-
assert data.shape == self.shape
|
109
|
-
assert data.dtype == np.float32
|
110
|
-
# Rectangular memcopy
|
111
|
-
# TODO profile, and if needed include this copy in the padding kernel
|
112
|
-
if isinstance(data, np.ndarray) or isinstance(data, self.cuda_processing.array_class):
|
113
|
-
self.d_radio_padded[: self.shape[0], : self.shape[1]] = data[:, :]
|
114
|
-
elif isinstance(data, cuda.DeviceAllocation):
|
115
|
-
# TODO manual memcpy2D
|
116
|
-
raise NotImplementedError("pycuda buffers are not supported yet")
|
117
|
-
else:
|
118
|
-
raise ValueError("Expected either numpy array, pycuda array or pycuda buffer")
|
119
|
-
|
120
|
-
def get_output(self, output):
|
121
|
-
s0, s1 = self.shape_inner
|
122
|
-
((U, _), (L, _)) = self.margin
|
123
|
-
if output is None:
|
124
|
-
# copy D2H
|
125
|
-
return self.d_radio_padded[U : U + s0, L : L + s1].get()
|
126
|
-
assert output.shape == self.shape_inner
|
127
|
-
assert output.dtype == np.float32
|
128
|
-
output[:, :] = self.d_radio_padded[U : U + s0, L : L + s1]
|
129
|
-
return output
|
130
|
-
|
131
|
-
def apply_filter(self, radio, output=None):
|
132
|
-
self.set_input(radio)
|
133
|
-
|
134
|
-
self.padding_kernel(*self.padding_kernel_args)
|
135
|
-
self.cufft.fft(self.d_radio_padded, output=self.d_radio_f)
|
136
|
-
self.cpxmult_kernel(*self.cpxmult_kernel_args)
|
137
|
-
self.cufft.ifft(self.d_radio_f, output=self.d_radio_padded)
|
138
|
-
|
139
|
-
return self.get_output(output)
|
140
|
-
|
141
|
-
__call__ = apply_filter
|
142
|
-
|
143
|
-
retrieve_phase = apply_filter
|
@@ -1,95 +0,0 @@
|
|
1
|
-
from math import floor
|
2
|
-
import numpy as np
|
3
|
-
|
4
|
-
|
5
|
-
class VerticalShift:
|
6
|
-
def __init__(self, radios_shape, shifts):
|
7
|
-
"""
|
8
|
-
This class is used when a vertical translation (along the tomography
|
9
|
-
rotation axis) occurred.
|
10
|
-
|
11
|
-
These translations are meant "per projection" and can be due either to
|
12
|
-
mechanical errors, or can be applied purposefully with known motor movements
|
13
|
-
to smear rings artefacts.
|
14
|
-
|
15
|
-
The object is initialised with an array of shifts: one shift for each projection.
|
16
|
-
A positive shifts means that the axis has moved in the positive Z direction.
|
17
|
-
The interpolation is done taking for a pixel (y,x) the pixel found at (y+shft,x)
|
18
|
-
in the recorded images.
|
19
|
-
|
20
|
-
The method apply_vertical_shifts performs the correctionson the radios.
|
21
|
-
|
22
|
-
Parameters
|
23
|
-
----------
|
24
|
-
radios_shape: tuple
|
25
|
-
Shape of the radios chunk, in the form (n_radios, n_y, n_x)
|
26
|
-
shifts: sequence of floats
|
27
|
-
one shift for each projection
|
28
|
-
|
29
|
-
Notes
|
30
|
-
------
|
31
|
-
During the acquisition, there might be other translations, each of them
|
32
|
-
orthogonal to the rotation axis.
|
33
|
-
- A "horizontal" translation in the detector plane: this is handled
|
34
|
-
directly in the Backprojection operation.
|
35
|
-
- A translation along the beam direction: this one is of no concern
|
36
|
-
for parallel-beam geometry
|
37
|
-
"""
|
38
|
-
self.radios_shape = radios_shape
|
39
|
-
self.shifts = shifts
|
40
|
-
self._init_interp_coefficients()
|
41
|
-
|
42
|
-
def _init_interp_coefficients(self):
|
43
|
-
self.interp_infos = []
|
44
|
-
for s in self.shifts:
|
45
|
-
s0 = int(floor(s))
|
46
|
-
f = s - s0
|
47
|
-
self.interp_infos.append([s0, f])
|
48
|
-
|
49
|
-
def _check(self, radios, iangles):
|
50
|
-
assert np.min(iangles) >= 0
|
51
|
-
assert np.max(iangles) < len(self.interp_infos)
|
52
|
-
assert len(iangles) == radios.shape[0]
|
53
|
-
|
54
|
-
def apply_vertical_shifts(self, radios, iangles, output=None):
|
55
|
-
"""
|
56
|
-
Parameters
|
57
|
-
----------
|
58
|
-
radios: a sequence of np.array
|
59
|
-
The input radios. If the optional parameter is not given, they are modified in-place
|
60
|
-
iangles: a sequence of integers
|
61
|
-
Must have the same lenght as radios.
|
62
|
-
It contains the index at which the shift is found in `self.shifts`
|
63
|
-
given by `shifts` argument in the initialisation of the object.
|
64
|
-
output: a sequence of np.array, optional
|
65
|
-
If given, it will be modified to contain the shifted radios.
|
66
|
-
Must be of the same shape of `radios`.
|
67
|
-
"""
|
68
|
-
self._check(radios, iangles)
|
69
|
-
|
70
|
-
newradio = np.zeros_like(radios[0])
|
71
|
-
for radio, ia in zip(radios, iangles):
|
72
|
-
newradio[:] = 0
|
73
|
-
S0, f = self.interp_infos[ia]
|
74
|
-
s0 = S0
|
75
|
-
|
76
|
-
if s0 > 0:
|
77
|
-
newradio[:-s0] = radio[s0:] * (1 - f)
|
78
|
-
elif s0 == 0:
|
79
|
-
newradio[:] = radio[s0:] * (1 - f)
|
80
|
-
else:
|
81
|
-
newradio[-s0:] = radio[:s0] * (1 - f)
|
82
|
-
|
83
|
-
s0 = S0 + 1
|
84
|
-
|
85
|
-
if s0 > 0:
|
86
|
-
newradio[:-s0] += radio[s0:] * f
|
87
|
-
elif s0 == 0:
|
88
|
-
newradio[:] += radio[s0:] * f
|
89
|
-
else:
|
90
|
-
newradio[-s0:] += radio[:s0] * f
|
91
|
-
|
92
|
-
if output is None:
|
93
|
-
radios[ia] = newradio
|
94
|
-
else:
|
95
|
-
output[ia] = newradio
|