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/app/parse_reconstruction_log.py +0 -151
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- build/lib/nabu/app/reduce_dark_flat.py +0 -181
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- build/lib/nabu/cuda/__init__.py +0 -0
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- build/lib/nabu/cuda/kernel.py +0 -97
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- build/lib/nabu/cuda/padding.py +0 -6
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- build/lib/nabu/io/tests/__init__.py +0 -0
- build/lib/nabu/io/tests/test_cast_volume.py +0 -339
- build/lib/nabu/io/tests/test_detector_distortion.py +0 -178
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- build/lib/nabu/misc/__init__.py +0 -0
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- build/lib/nabu/misc/rotation_cuda.py +0 -6
- build/lib/nabu/misc/tests/__init__.py +0 -1
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- build/lib/nabu/pipeline/detector_distortion_provider.py +0 -20
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- build/lib/nabu/pipeline/xrdct/__init__.py +0 -0
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- build/lib/nabu/preproc/tests/test_ccd_corr.py +0 -59
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- build/lib/nabu/preproc/tests/test_double_flatfield.py +0 -86
- build/lib/nabu/preproc/tests/test_flatfield.py +0 -626
- build/lib/nabu/preproc/tests/test_paganin.py +0 -67
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- build/lib/nabu/processing/fftshift.py +0 -134
- build/lib/nabu/processing/histogram.py +0 -286
- build/lib/nabu/processing/histogram_cuda.py +0 -103
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- build/lib/nabu/processing/medfilt_cuda.py +0 -159
- build/lib/nabu/processing/muladd.py +0 -29
- build/lib/nabu/processing/muladd_cuda.py +0 -68
- build/lib/nabu/processing/padding_base.py +0 -71
- build/lib/nabu/processing/padding_cuda.py +0 -75
- build/lib/nabu/processing/padding_opencl.py +0 -77
- 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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|
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def _get_nabu_environment_variables():
|
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return nabu_env_settings
|
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|
@@ -1,193 +0,0 @@
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from os import path
|
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from tomoscan.esrf import TIFFVolume, MultiTIFFVolume, EDFVolume, JP2KVolume
|
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from ..utils import check_supported, get_num_threads
|
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from ..resources.logger import LoggerOrPrint
|
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from ..io.writer import NXProcessWriter, HSTVolVolume, NXVolVolume
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from ..io.utils import convert_dict_values
|
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from .params import files_formats
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class WriterManager:
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"""
|
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This class is a wrapper on top of all "writers".
|
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It will create the right "writer" with all the necessary options, and the histogram writer.
|
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|
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The layout is the following.
|
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|
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* Single-big-file volume formats (big-tiff, .vol):
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- no start index
|
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- everything is increasingly written in one file
|
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* Multiple-frames per file (HDF5 + master-file):
|
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- needs a start index (change file_prefix) for each partial file
|
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- needs a subdirectory for partial files
|
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* One-file-per-frame (tiff, edf, jp2)
|
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- start_index
|
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|
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When saving intermediate steps (eg. sinogram): HDF5 format is always used.
|
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"""
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|
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_overwrite_warned = False
|
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_writer_classes = {
|
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"hdf5": NXVolVolume,
|
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"tiff": TIFFVolume,
|
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"bigtiff": MultiTIFFVolume,
|
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"jp2": JP2KVolume,
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"edf": EDFVolume,
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"vol": HSTVolVolume,
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}
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|
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def __init__(
|
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self,
|
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output_dir,
|
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file_prefix,
|
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file_format="hdf5",
|
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overwrite=False,
|
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start_index=0,
|
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logger=None,
|
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metadata=None,
|
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histogram=False,
|
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extra_options=None,
|
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):
|
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"""
|
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Create a Writer from a set of parameters.
|
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|
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Parameters
|
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----------
|
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output_dir: str
|
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Directory where the file(s) will be written.
|
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file_prefix: str
|
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File prefix (without leading path)
|
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start_index: int, optional
|
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Index to start the files numbering (filename_0123.ext).
|
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Default is 0.
|
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Ignored for HDF5 extension.
|
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logger: nabu.resources.logger.Logger, optional
|
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Logger object
|
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metadata: dict, optional
|
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Metadata, eg. information on various processing steps. For HDF5, it will go to "configuration"
|
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histogram: bool, optional
|
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Whether to also write a histogram of data. If set to True, it will configure
|
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an additional "writer".
|
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extra_options: dict, optional
|
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Other advanced options to pass to Writer class.
|
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"""
|
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|
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self.extra_options = extra_options or {}
|
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self._set_file_format(file_format)
|
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self.overwrite = overwrite
|
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|
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self.start_index = start_index
|
79
|
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self.logger = LoggerOrPrint(logger)
|
80
|
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self.histogram = histogram
|
81
|
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self.output_dir = output_dir
|
82
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self.file_prefix = file_prefix
|
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|
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self.metadata = convert_dict_values(metadata or {}, {None: "None"})
|
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|
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self._init_writer()
|
85
|
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self._init_histogram_writer()
|
86
|
-
|
87
|
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def _set_file_format(self, file_format):
|
88
|
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check_supported(file_format, files_formats, "file format")
|
89
|
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self.file_format = files_formats[file_format]
|
90
|
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self._is_bigtiff = file_format in ["tiff", "tif"] and any(
|
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[self.extra_options.get(opt, False) for opt in ["tiff_single_file", "use_bigtiff"]]
|
92
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)
|
93
|
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if self._is_bigtiff:
|
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|
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self.file_format = "bigtiff"
|
95
|
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|
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|
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@staticmethod
|
97
|
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def get_first_fname(vol_writer):
|
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|
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if hasattr(vol_writer, "file_path"):
|
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|
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return path.dirname(vol_writer.file_path)
|
100
|
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dirname = vol_writer.data_url.file_path()
|
101
|
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fname = vol_writer.data_url.data_path().format(
|
102
|
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volume_basename=vol_writer._volume_basename,
|
103
|
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index_zfill6=vol_writer.start_index,
|
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|
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data_extension=vol_writer.extension or vol_writer.DEFAULT_DATA_EXTENSION,
|
105
|
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)
|
106
|
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return path.join(dirname, fname)
|
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|
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|
108
|
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@staticmethod
|
109
|
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def get_fname(vol_writer):
|
110
|
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if hasattr(vol_writer, "file_path"):
|
111
|
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# several frames per file - return the file itself
|
112
|
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return vol_writer.file_path
|
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|
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# one file per frame - return the directory
|
114
|
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return vol_writer.data_url.file_path()
|
115
|
-
|
116
|
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def _init_writer(self):
|
117
|
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if self.file_format in ["tiff", "edf", "jp2", "hdf5"]:
|
118
|
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writer_kwargs = {
|
119
|
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"folder": self.output_dir,
|
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|
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"volume_basename": self.file_prefix,
|
121
|
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"start_index": self.start_index,
|
122
|
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"overwrite": self.overwrite,
|
123
|
-
}
|
124
|
-
if self.file_format == "hdf5":
|
125
|
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writer_kwargs["data_path"] = self.metadata.get("entry", "entry")
|
126
|
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writer_kwargs["process_name"] = self.metadata.get("process_name", "reconstruction")
|
127
|
-
writer_kwargs["create_subfolder"] = self.extra_options.get("create_subfolder", True)
|
128
|
-
elif self.file_format == "jp2":
|
129
|
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writer_kwargs["cratios"] = self.metadata.get("jpeg2000_compression_ratio", None)
|
130
|
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writer_kwargs["clip_values"] = self.metadata.get("float_clip_values", None)
|
131
|
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writer_kwargs["n_threads"] = get_num_threads()
|
132
|
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elif self.file_format in ["vol", "bigtiff"]:
|
133
|
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writer_kwargs = {
|
134
|
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"file_path": path.join(
|
135
|
-
self.output_dir, self.file_prefix + "." + self.file_format.replace("bigtiff", "tiff")
|
136
|
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),
|
137
|
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"overwrite": self.overwrite,
|
138
|
-
"append": self.extra_options.get("single_output_file_initialized", False),
|
139
|
-
"hst_metadata": self.extra_options.get("raw_vol_metadata", {}),
|
140
|
-
}
|
141
|
-
else:
|
142
|
-
raise ValueError("Unsupported file format: %s" % self.file_format)
|
143
|
-
self._h5_entry = self.metadata.get("entry", "entry")
|
144
|
-
self.writer = self._writer_classes[self.file_format](**writer_kwargs)
|
145
|
-
self.fname = self.get_fname(self.writer)
|
146
|
-
if path.exists(self.fname):
|
147
|
-
err = "File already exists: %s" % self.fname
|
148
|
-
if self.overwrite:
|
149
|
-
if not (self.__class__._overwrite_warned):
|
150
|
-
self.logger.warning(err + ". It will be overwritten as requested in configuration")
|
151
|
-
self.__class__._overwrite_warned = True
|
152
|
-
else:
|
153
|
-
self.logger.fatal(err)
|
154
|
-
raise ValueError(err)
|
155
|
-
|
156
|
-
def _init_histogram_writer(self):
|
157
|
-
if not self.histogram:
|
158
|
-
return
|
159
|
-
separate_histogram_file = not (self.file_format == "hdf5")
|
160
|
-
if separate_histogram_file:
|
161
|
-
fmode = "w"
|
162
|
-
hist_fname = path.join(self.output_dir, "histogram_%05d.hdf5" % self.start_index)
|
163
|
-
else:
|
164
|
-
fmode = "a"
|
165
|
-
hist_fname = self.fname
|
166
|
-
# Nabu's original NXProcessWriter has to be used here, as histogram is not 3D
|
167
|
-
self.histogram_writer = NXProcessWriter(
|
168
|
-
hist_fname,
|
169
|
-
entry=self._h5_entry,
|
170
|
-
filemode=fmode,
|
171
|
-
overwrite=True,
|
172
|
-
)
|
173
|
-
|
174
|
-
def write_histogram(self, data, config=None, processing_index=1):
|
175
|
-
if not (self.histogram):
|
176
|
-
return
|
177
|
-
self.histogram_writer.write(
|
178
|
-
data,
|
179
|
-
"histogram",
|
180
|
-
processing_index=processing_index,
|
181
|
-
config=config,
|
182
|
-
is_frames_stack=False,
|
183
|
-
direct_access=False,
|
184
|
-
)
|
185
|
-
|
186
|
-
def _write_metadata(self):
|
187
|
-
self.writer.metadata = self.metadata
|
188
|
-
self.writer.save_metadata()
|
189
|
-
|
190
|
-
def write_data(self, data):
|
191
|
-
self.writer.data = data
|
192
|
-
self.writer.save()
|
193
|
-
# self._write_metadata()
|
File without changes
|
@@ -1,7 +0,0 @@
|
|
1
|
-
from .ccd import CCDFilter, Log
|
2
|
-
from .ctf import CTFPhaseRetrieval
|
3
|
-
from .distortion import DistortionCorrection
|
4
|
-
from .double_flatfield import DoubleFlatField
|
5
|
-
from .flatfield import FlatField, FlatFieldDataUrls
|
6
|
-
from .phase import PaganinPhaseRetrieval
|
7
|
-
from .shift import VerticalShift
|
@@ -1,11 +0,0 @@
|
|
1
|
-
# Backward compat.
|
2
|
-
from ..estimation.alignment import AlignmentBase
|
3
|
-
from ..estimation.cor import (
|
4
|
-
CenterOfRotation,
|
5
|
-
CenterOfRotationAdaptiveSearch,
|
6
|
-
CenterOfRotationGrowingWindow,
|
7
|
-
CenterOfRotationSlidingWindow,
|
8
|
-
)
|
9
|
-
from ..estimation.translation import DetectorTranslationAlongBeam
|
10
|
-
from ..estimation.focus import CameraFocus
|
11
|
-
from ..estimation.tilt import CameraTilt
|
@@ -1,161 +0,0 @@
|
|
1
|
-
import numpy as np
|
2
|
-
from ..utils import check_supported
|
3
|
-
from silx.math.medianfilter import medfilt2d
|
4
|
-
|
5
|
-
|
6
|
-
class CCDFilter:
|
7
|
-
"""
|
8
|
-
Filtering applied on radios.
|
9
|
-
"""
|
10
|
-
|
11
|
-
_supported_ccd_corrections = ["median_clip"]
|
12
|
-
|
13
|
-
def __init__(
|
14
|
-
self,
|
15
|
-
radios_shape: tuple,
|
16
|
-
correction_type: str = "median_clip",
|
17
|
-
median_clip_thresh: float = 0.1,
|
18
|
-
abs_diff=False,
|
19
|
-
preserve_borders=False,
|
20
|
-
):
|
21
|
-
"""
|
22
|
-
Initialize a CCDCorrection instance.
|
23
|
-
|
24
|
-
Parameters
|
25
|
-
-----------
|
26
|
-
radios_shape: tuple
|
27
|
-
A tuple describing the shape of the radios stack, in the form
|
28
|
-
`(n_radios, n_z, n_x)`.
|
29
|
-
correction_type: str
|
30
|
-
Correction type for radios ("median_clip", "sigma_clip", ...)
|
31
|
-
median_clip_thresh: float, optional
|
32
|
-
Threshold for the median clipping method.
|
33
|
-
abs_diff: boolean
|
34
|
-
by default False: the correction is triggered when img - median > threshold.
|
35
|
-
If equals True: correction is triggered for abs(img-media) > threshold
|
36
|
-
preserve borders: boolean
|
37
|
-
by default False:
|
38
|
-
If equals True: the borders (width=1) are not modified.
|
39
|
-
|
40
|
-
|
41
|
-
Notes
|
42
|
-
------
|
43
|
-
A CCD correction is a process (usually filtering) taking place in the
|
44
|
-
radios space.
|
45
|
-
Available filters:
|
46
|
-
- median_clip: if the value of the current pixel exceeds the median
|
47
|
-
of adjacent pixels (a 3x3 neighborhood) more than a threshold,
|
48
|
-
then this pixel value is set to the median value.
|
49
|
-
"""
|
50
|
-
self._set_radios_shape(radios_shape)
|
51
|
-
check_supported(correction_type, self._supported_ccd_corrections, "CCD correction mode")
|
52
|
-
self.correction_type = correction_type
|
53
|
-
self.median_clip_thresh = median_clip_thresh
|
54
|
-
self.abs_diff = abs_diff
|
55
|
-
self.preserve_borders = preserve_borders
|
56
|
-
|
57
|
-
def _set_radios_shape(self, radios_shape):
|
58
|
-
if len(radios_shape) == 2:
|
59
|
-
self.radios_shape = (1,) + radios_shape
|
60
|
-
elif len(radios_shape) == 3:
|
61
|
-
self.radios_shape = radios_shape
|
62
|
-
else:
|
63
|
-
raise ValueError("Expected radios to have 2 or 3 dimensions")
|
64
|
-
n_radios, n_z, n_x = self.radios_shape
|
65
|
-
self.n_radios = n_radios
|
66
|
-
self.n_angles = n_radios
|
67
|
-
self.shape = (n_z, n_x)
|
68
|
-
|
69
|
-
@staticmethod
|
70
|
-
def median_filter(img):
|
71
|
-
"""
|
72
|
-
Perform a median filtering on an image.
|
73
|
-
"""
|
74
|
-
return medfilt2d(img, (3, 3), mode="reflect")
|
75
|
-
|
76
|
-
def median_clip_mask(self, img, return_medians=False):
|
77
|
-
"""
|
78
|
-
Compute a mask indicating whether a pixel is valid or not, according to
|
79
|
-
the median-clip method.
|
80
|
-
|
81
|
-
Parameters
|
82
|
-
----------
|
83
|
-
img: numpy.ndarray
|
84
|
-
Input image
|
85
|
-
return_medians: bool, optional
|
86
|
-
Whether to return the median values additionally to the mask.
|
87
|
-
"""
|
88
|
-
median_values = self.median_filter(img)
|
89
|
-
if not self.abs_diff:
|
90
|
-
invalid_mask = img >= median_values + self.median_clip_thresh
|
91
|
-
else:
|
92
|
-
invalid_mask = abs(img - median_values) > self.median_clip_thresh
|
93
|
-
|
94
|
-
if return_medians:
|
95
|
-
return invalid_mask, median_values
|
96
|
-
else:
|
97
|
-
return invalid_mask
|
98
|
-
|
99
|
-
def median_clip_correction(self, radio, output=None):
|
100
|
-
"""
|
101
|
-
Compute the median clip correction on one image.
|
102
|
-
|
103
|
-
Parameters
|
104
|
-
----------
|
105
|
-
radios: numpy.ndarray, optional
|
106
|
-
A radio image.
|
107
|
-
output: numpy.ndarray, optional
|
108
|
-
Output array
|
109
|
-
"""
|
110
|
-
assert radio.shape == self.shape
|
111
|
-
if output is None:
|
112
|
-
output = np.copy(radio)
|
113
|
-
else:
|
114
|
-
output[:] = radio[:]
|
115
|
-
invalid_mask, medians = self.median_clip_mask(radio, return_medians=True)
|
116
|
-
|
117
|
-
if self.preserve_borders:
|
118
|
-
fixed_border = np.array(radio[[0, 0, -1, -1], [0, -1, 0, -1]])
|
119
|
-
|
120
|
-
output[invalid_mask] = medians[invalid_mask]
|
121
|
-
|
122
|
-
if self.preserve_borders:
|
123
|
-
output[[0, 0, -1, -1], [0, -1, 0, -1]] = fixed_border
|
124
|
-
|
125
|
-
return output
|
126
|
-
|
127
|
-
|
128
|
-
class Log:
|
129
|
-
"""
|
130
|
-
Helper class to take -log(radios)
|
131
|
-
|
132
|
-
Parameters
|
133
|
-
-----------
|
134
|
-
clip_min: float, optional
|
135
|
-
Before taking the logarithm, the values are clipped to this minimum.
|
136
|
-
clip_max: float, optional
|
137
|
-
Before taking the logarithm, the values are clipped to this maximum.
|
138
|
-
"""
|
139
|
-
|
140
|
-
def __init__(self, radios_shape, clip_min=None, clip_max=None):
|
141
|
-
self.radios_shape = radios_shape
|
142
|
-
self.clip_min = clip_min
|
143
|
-
self.clip_max = clip_max
|
144
|
-
|
145
|
-
def take_logarithm(self, radios):
|
146
|
-
"""
|
147
|
-
Take the negative logarithm of a radios chunk.
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Processing is done in-place !
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Parameters
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-----------
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radios: array
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Radios chunk.
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"""
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if (self.clip_min is not None) or (self.clip_max is not None):
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np.clip(radios, self.clip_min, self.clip_max, out=radios)
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np.log(radios, out=radios)
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else:
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np.log(radios, out=radios)
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radios[:] *= -1
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return radios
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@@ -1,169 +0,0 @@
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import numpy as np
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from ..preproc.ccd import CCDFilter, Log
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from ..processing.medfilt_cuda import MedianFilter
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from ..utils import get_cuda_srcfile, updiv, deprecated_class
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from ..cuda.utils import __has_pycuda__
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if __has_pycuda__:
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from ..cuda.kernel import CudaKernel
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# COMPAT.
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from .flatfield_cuda import (
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CudaFlatField as CudaFlatfield_,
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CudaFlatFieldArrays as CudaFlatFieldArrays_,
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CudaFlatFieldDataUrls as CudaFlatFieldDataUrls_,
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)
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FlatField = deprecated_class(
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"preproc.ccd_cuda.CudaFlatField was moved to preproc.flatfield_cuda.CudaFlatField", do_print=True
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)(CudaFlatfield_)
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FlatFieldArrays = deprecated_class(
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"preproc.ccd_cuda.CudaFlatFieldArrays was moved to preproc.flatfield_cuda.CudaFlatFieldArrays", do_print=True
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)(CudaFlatFieldArrays_)
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FlatFieldDataUrls = deprecated_class(
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"preproc.ccd_cuda.CudaFlatFieldDataUrls was moved to preproc.flatfield_cuda.CudaFlatFieldDataUrls", do_print=True
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)(CudaFlatFieldDataUrls_)
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#
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class CudaCCDFilter(CCDFilter):
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def __init__(
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self,
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radios_shape,
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correction_type="median_clip",
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median_clip_thresh=0.1,
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abs_diff=False,
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cuda_options=None,
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):
|
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"""
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Initialize a CudaCCDCorrection instance.
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Please refer to the documentation of CCDCorrection.
|
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"""
|
42
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super().__init__(
|
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radios_shape,
|
44
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correction_type=correction_type,
|
45
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median_clip_thresh=median_clip_thresh,
|
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)
|
47
|
-
self._set_cuda_options(cuda_options)
|
48
|
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self.cuda_median_filter = None
|
49
|
-
if correction_type == "median_clip":
|
50
|
-
self.cuda_median_filter = MedianFilter(
|
51
|
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self.shape,
|
52
|
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footprint=(3, 3),
|
53
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mode="reflect",
|
54
|
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threshold=median_clip_thresh,
|
55
|
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abs_diff=abs_diff,
|
56
|
-
cuda_options={
|
57
|
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"device_id": self.cuda_options["device_id"],
|
58
|
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"ctx": self.cuda_options["ctx"],
|
59
|
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"cleanup_at_exit": self.cuda_options["cleanup_at_exit"],
|
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|
-
},
|
61
|
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)
|
62
|
-
|
63
|
-
def _set_cuda_options(self, user_cuda_options):
|
64
|
-
self.cuda_options = {"device_id": None, "ctx": None, "cleanup_at_exit": None}
|
65
|
-
if user_cuda_options is None:
|
66
|
-
user_cuda_options = {}
|
67
|
-
self.cuda_options.update(user_cuda_options)
|
68
|
-
|
69
|
-
def median_clip_correction(self, radio, output=None):
|
70
|
-
"""
|
71
|
-
Compute the median clip correction on one image.
|
72
|
-
|
73
|
-
Parameters
|
74
|
-
----------
|
75
|
-
radio: pycuda.gpuarray
|
76
|
-
A radio image
|
77
|
-
output: pycuda.gpuarray, optional
|
78
|
-
Output data.
|
79
|
-
"""
|
80
|
-
assert radio.shape == self.shape
|
81
|
-
return self.cuda_median_filter.medfilt2(radio, output=output)
|
82
|
-
|
83
|
-
|
84
|
-
CudaCCDCorrection = deprecated_class("CudaCCDCorrection is replaced with CudaCCDFilter", do_print=True)(CudaCCDFilter)
|
85
|
-
|
86
|
-
|
87
|
-
class CudaLog(Log):
|
88
|
-
"""
|
89
|
-
Helper class to take -log(radios)
|
90
|
-
"""
|
91
|
-
|
92
|
-
def __init__(self, radios_shape, clip_min=None, clip_max=None):
|
93
|
-
"""
|
94
|
-
Initialize a Log processing.
|
95
|
-
|
96
|
-
Parameters
|
97
|
-
-----------
|
98
|
-
radios_shape: tuple
|
99
|
-
The shape of 3D radios stack.
|
100
|
-
clip_min: float, optional
|
101
|
-
Data smaller than this value is replaced by this value.
|
102
|
-
clip_max: float, optional.
|
103
|
-
Data bigger than this value is replaced by this value.
|
104
|
-
"""
|
105
|
-
super().__init__(radios_shape, clip_min=clip_min, clip_max=clip_max)
|
106
|
-
self._init_kernels()
|
107
|
-
|
108
|
-
def _init_kernels(self):
|
109
|
-
self._do_clip_min = int(self.clip_min is not None)
|
110
|
-
self._do_clip_max = int(self.clip_max is not None)
|
111
|
-
self.clip_min = np.float32(self.clip_min or 0)
|
112
|
-
self.clip_max = np.float32(self.clip_max or 1)
|
113
|
-
self._nlog_srcfile = get_cuda_srcfile("ElementOp.cu")
|
114
|
-
nz, ny, nx = self.radios_shape
|
115
|
-
self._nx = np.int32(nx)
|
116
|
-
self._ny = np.int32(ny)
|
117
|
-
self._nz = np.int32(nz)
|
118
|
-
self._nthreadsperblock = (16, 16, 4) # TODO tune ?
|
119
|
-
self._nblocks = tuple([updiv(n, p) for n, p in zip([nx, ny, nz], self._nthreadsperblock)])
|
120
|
-
|
121
|
-
self.nlog_kernel = CudaKernel(
|
122
|
-
"nlog",
|
123
|
-
filename=self._nlog_srcfile,
|
124
|
-
signature="Piiiff",
|
125
|
-
options=[
|
126
|
-
"-DDO_CLIP_MIN=%d" % self._do_clip_min,
|
127
|
-
"-DDO_CLIP_MAX=%d" % self._do_clip_max,
|
128
|
-
],
|
129
|
-
)
|
130
|
-
|
131
|
-
def take_logarithm(self, radios, clip_min=None, clip_max=None):
|
132
|
-
"""
|
133
|
-
Take the negative logarithm of a radios chunk.
|
134
|
-
|
135
|
-
Parameters
|
136
|
-
-----------
|
137
|
-
radios: `pycuda.gpuarray.GPUArray`
|
138
|
-
Radios chunk
|
139
|
-
If not provided, a new GPU array is created.
|
140
|
-
clip_min: float, optional
|
141
|
-
Before taking the logarithm, the values are clipped to this minimum.
|
142
|
-
clip_max: float, optional
|
143
|
-
Before taking the logarithm, the values are clipped to this maximum.
|
144
|
-
"""
|
145
|
-
clip_min = clip_min or self.clip_min
|
146
|
-
clip_max = clip_max or self.clip_max
|
147
|
-
if radios.flags.c_contiguous:
|
148
|
-
self.nlog_kernel(
|
149
|
-
radios,
|
150
|
-
self._nx,
|
151
|
-
self._ny,
|
152
|
-
self._nz,
|
153
|
-
clip_min,
|
154
|
-
clip_max,
|
155
|
-
grid=self._nblocks,
|
156
|
-
block=self._nthreadsperblock,
|
157
|
-
)
|
158
|
-
else:
|
159
|
-
# map-like operations cannot be directly applied on 3D arrays
|
160
|
-
# that are not C-contiguous. We have to process image per image.
|
161
|
-
# TODO it's even worse when each single frame is not C-contiguous. For now this case is not handled
|
162
|
-
nz = np.int32(1)
|
163
|
-
nthreadsperblock = (32, 32, 1)
|
164
|
-
nblocks = tuple([updiv(n, p) for n, p in zip([int(self._nx), int(self._ny), int(nz)], nthreadsperblock)])
|
165
|
-
for i in range(radios.shape[0]):
|
166
|
-
self.nlog_kernel(
|
167
|
-
radios[i], self._nx, self._ny, nz, clip_min, clip_max, grid=nblocks, block=nthreadsperblock
|
168
|
-
)
|
169
|
-
return radios
|