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
- build/lib/nabu/app/prepare_weights_double.py +0 -163
- build/lib/nabu/app/reconstruct.py +0 -120
- build/lib/nabu/app/reconstruct_helical.py +0 -116
- build/lib/nabu/app/reduce_dark_flat.py +0 -181
- build/lib/nabu/app/rotate.py +0 -162
- build/lib/nabu/app/shrink_dataset.py +0 -98
- build/lib/nabu/app/stitching.py +0 -85
- build/lib/nabu/app/tests/test_reduce_dark_flat.py +0 -78
- build/lib/nabu/app/utils.py +0 -33
- build/lib/nabu/app/validator.py +0 -110
- build/lib/nabu/cuda/__init__.py +0 -0
- build/lib/nabu/cuda/convolution.py +0 -8
- build/lib/nabu/cuda/fft.py +0 -4
- build/lib/nabu/cuda/kernel.py +0 -97
- build/lib/nabu/cuda/medfilt.py +0 -6
- build/lib/nabu/cuda/padding.py +0 -6
- build/lib/nabu/cuda/processing.py +0 -75
- build/lib/nabu/cuda/tests/__init__.py +0 -1
- build/lib/nabu/cuda/utils.py +0 -331
- build/lib/nabu/estimation/__init__.py +0 -12
- build/lib/nabu/estimation/alignment.py +0 -578
- build/lib/nabu/estimation/cor.py +0 -1621
- build/lib/nabu/estimation/cor_sino.py +0 -183
- build/lib/nabu/estimation/distortion.py +0 -112
- build/lib/nabu/estimation/focus.py +0 -362
- build/lib/nabu/estimation/tests/__init__.py +0 -0
- build/lib/nabu/estimation/tests/test_alignment.py +0 -70
- build/lib/nabu/estimation/tests/test_cor.py +0 -472
- build/lib/nabu/estimation/tests/test_focus.py +0 -105
- build/lib/nabu/estimation/tests/test_tilt.py +0 -41
- build/lib/nabu/estimation/tests/test_translation.py +0 -78
- build/lib/nabu/estimation/tilt.py +0 -214
- build/lib/nabu/estimation/translation.py +0 -193
- build/lib/nabu/estimation/utils.py +0 -39
- build/lib/nabu/io/__init__.py +0 -2
- build/lib/nabu/io/cast_volume.py +0 -371
- build/lib/nabu/io/detector_distortion.py +0 -305
- build/lib/nabu/io/reader.py +0 -628
- build/lib/nabu/io/reader_helical.py +0 -114
- 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
- build/lib/nabu/io/tests/test_writers.py +0 -187
- build/lib/nabu/io/tiffwriter_zmm.py +0 -99
- build/lib/nabu/io/utils.py +0 -263
- build/lib/nabu/io/writer.py +0 -892
- build/lib/nabu/misc/__init__.py +0 -0
- build/lib/nabu/misc/binning.py +0 -98
- build/lib/nabu/misc/fftshift.py +0 -6
- build/lib/nabu/misc/filters.py +0 -24
- build/lib/nabu/misc/fourier_filters.py +0 -152
- build/lib/nabu/misc/histogram.py +0 -6
- build/lib/nabu/misc/histogram_cuda.py +0 -8
- build/lib/nabu/misc/kernel_base.py +0 -4
- build/lib/nabu/misc/padding.py +0 -83
- build/lib/nabu/misc/padding_base.py +0 -6
- build/lib/nabu/misc/processing_base.py +0 -4
- build/lib/nabu/misc/rotation.py +0 -6
- build/lib/nabu/misc/rotation_cuda.py +0 -6
- build/lib/nabu/misc/tests/__init__.py +0 -1
- build/lib/nabu/misc/tests/test_binning.py +0 -48
- build/lib/nabu/misc/tests/test_interpolation.py +0 -70
- build/lib/nabu/misc/transpose.py +0 -6
- build/lib/nabu/misc/unsharp.py +0 -4
- build/lib/nabu/misc/unsharp_cuda.py +0 -6
- build/lib/nabu/misc/unsharp_opencl.py +0 -8
- build/lib/nabu/misc/utils.py +0 -117
- build/lib/nabu/opencl/__init__.py +0 -0
- build/lib/nabu/opencl/fft.py +0 -6
- build/lib/nabu/opencl/kernel.py +0 -135
- build/lib/nabu/opencl/memcpy.py +0 -35
- build/lib/nabu/opencl/padding.py +0 -6
- build/lib/nabu/opencl/processing.py +0 -62
- build/lib/nabu/opencl/tests/__init__.py +0 -0
- build/lib/nabu/opencl/utils.py +0 -292
- build/lib/nabu/pipeline/__init__.py +0 -0
- build/lib/nabu/pipeline/config.py +0 -265
- build/lib/nabu/pipeline/config_validators.py +0 -589
- build/lib/nabu/pipeline/datadump.py +0 -164
- build/lib/nabu/pipeline/dataset_validator.py +0 -211
- build/lib/nabu/pipeline/detector_distortion_provider.py +0 -20
- build/lib/nabu/pipeline/estimators.py +0 -1012
- build/lib/nabu/pipeline/fallback_utils.py +0 -149
- build/lib/nabu/pipeline/fullfield/__init__.py +0 -0
- build/lib/nabu/pipeline/fullfield/chunked.py +0 -849
- build/lib/nabu/pipeline/fullfield/chunked_cuda.py +0 -152
- build/lib/nabu/pipeline/fullfield/computations.py +0 -260
- build/lib/nabu/pipeline/fullfield/dataset_validator.py +0 -63
- build/lib/nabu/pipeline/fullfield/nabu_config.py +0 -590
- build/lib/nabu/pipeline/fullfield/processconfig.py +0 -825
- build/lib/nabu/pipeline/fullfield/reconstruction.py +0 -851
- build/lib/nabu/pipeline/helical/__init__.py +0 -0
- build/lib/nabu/pipeline/helical/dataset_validator.py +0 -19
- build/lib/nabu/pipeline/helical/fbp.py +0 -147
- build/lib/nabu/pipeline/helical/filtering.py +0 -246
- build/lib/nabu/pipeline/helical/gridded_accumulator.py +0 -575
- build/lib/nabu/pipeline/helical/helical_chunked_regridded.py +0 -1670
- build/lib/nabu/pipeline/helical/helical_chunked_regridded_cuda.py +0 -119
- build/lib/nabu/pipeline/helical/helical_reconstruction.py +0 -598
- build/lib/nabu/pipeline/helical/helical_utils.py +0 -42
- build/lib/nabu/pipeline/helical/nabu_config.py +0 -175
- build/lib/nabu/pipeline/helical/processconfig.py +0 -62
- build/lib/nabu/pipeline/helical/span_strategy.py +0 -483
- build/lib/nabu/pipeline/helical/tests/__init__.py +0 -0
- build/lib/nabu/pipeline/helical/tests/test_accumulator.py +0 -157
- build/lib/nabu/pipeline/helical/tests/test_pipeline_elements_full.py +0 -355
- build/lib/nabu/pipeline/helical/tests/test_strategy.py +0 -61
- build/lib/nabu/pipeline/helical/utils.py +0 -51
- build/lib/nabu/pipeline/helical/weight_balancer.py +0 -101
- build/lib/nabu/pipeline/params.py +0 -163
- build/lib/nabu/pipeline/processconfig.py +0 -210
- build/lib/nabu/pipeline/tests/test_chunk_reader.py +0 -78
- build/lib/nabu/pipeline/tests/test_estimators.py +0 -149
- build/lib/nabu/pipeline/utils.py +0 -116
- build/lib/nabu/pipeline/writer.py +0 -193
- build/lib/nabu/pipeline/xrdct/__init__.py +0 -0
- build/lib/nabu/preproc/__init__.py +0 -7
- build/lib/nabu/preproc/alignment.py +0 -11
- build/lib/nabu/preproc/ccd.py +0 -161
- build/lib/nabu/preproc/ccd_cuda.py +0 -169
- build/lib/nabu/preproc/ctf.py +0 -361
- build/lib/nabu/preproc/ctf_cuda.py +0 -142
- build/lib/nabu/preproc/distortion.py +0 -92
- build/lib/nabu/preproc/double_flatfield.py +0 -212
- build/lib/nabu/preproc/double_flatfield_cuda.py +0 -174
- build/lib/nabu/preproc/double_flatfield_variable_region.py +0 -68
- build/lib/nabu/preproc/flatfield.py +0 -448
- build/lib/nabu/preproc/flatfield_cuda.py +0 -144
- build/lib/nabu/preproc/flatfield_variable_region.py +0 -79
- build/lib/nabu/preproc/phase.py +0 -425
- build/lib/nabu/preproc/phase_cuda.py +0 -143
- build/lib/nabu/preproc/shift.py +0 -95
- build/lib/nabu/preproc/shift_cuda.py +0 -102
- build/lib/nabu/preproc/tests/__init__.py +0 -1
- build/lib/nabu/preproc/tests/test_ccd_corr.py +0 -59
- build/lib/nabu/preproc/tests/test_ctf.py +0 -250
- 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
- build/lib/nabu/preproc/tests/test_vshift.py +0 -73
- build/lib/nabu/processing/__init__.py +0 -0
- build/lib/nabu/processing/convolution_cuda.py +0 -375
- build/lib/nabu/processing/fft_base.py +0 -163
- build/lib/nabu/processing/fft_cuda.py +0 -256
- build/lib/nabu/processing/fft_opencl.py +0 -54
- 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
- build/lib/nabu/processing/kernel_base.py +0 -126
- 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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from scipy.ndimage import shift as ndshift
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from nabu.preproc.shift_cuda import CudaVerticalShift
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def bootstrap(request):
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cls = request.cls
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data = np.zeros([13, 11], "f")
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slope = 100 + np.arange(13)
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data[:] = slope[:, None]
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cls.radios = np.array([data] * 17)
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cls.shifts = 0.3 + np.arange(17)
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) # needs padding because ndshifs does not work as expected
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shifted_padded_radio = ndshift(padded_radio, [-my_shift, 0], mode="constant", cval=0.0, order=1).astype("f")
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golden.append(shifted_radio)
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cls.golden = np.array(golden)
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Shifter = VerticalShift(radios.shape, self.shifts)
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assert abs(radios - self.golden).max() < self.tol
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def test_cuda_vshift(self):
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d_radios = garray.to_gpu(self.radios)
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# Test with negative shifts
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Shifter_neg_cuda = CudaVerticalShift(d_radios.shape, -self.shifts)
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Shifter_neg_cuda.apply_vertical_shifts(d_radios2, self.indexes)
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err_max = np.max(np.abs(d_radios2.get() - radios2))
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assert err_max < 1e-6, "Something wrong for negative translations: max error = %.2e" % err_max
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import numpy as np
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"""
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A class for performing convolution on GPU with CUDA, but without using
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textures (unlike for example in ``silx.opencl.convolution``)
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"""
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def __init__(self, shape, kernel, axes=None, mode=None, extra_options=None, cuda_options=None):
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"""
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Constructor of Cuda Convolution.
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Parameters
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-----------
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shape: tuple
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Shape of the array.
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kernel: array-like
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Convolution kernel (1D, 2D or 3D).
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axes: tuple, optional
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Axes along which the convolution is performed,
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for batched convolutions.
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mode: str, optional
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Boundary handling mode. Available modes are:
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- "reflect": cba|abcd|dcb
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- "nearest": aaa|abcd|ddd
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- "wrap": bcd|abcd|abc
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- "constant": 000|abcd|000
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Default is "reflect".
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extra_options: dict, optional
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Advanced options (dict). Current options are:
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- "allocate_input_array": True
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- "allocate_output_array": True
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- "allocate_tmp_array": True
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- "sourcemodule_kwargs": {}
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- "batch_along_flat_dims": True
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"""
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self.cuda = CudaProcessing(**(cuda_options or {}))
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self._configure_extra_options(extra_options)
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self._determine_use_case(shape, kernel, axes)
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self._allocate_memory(mode)
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self._init_kernels()
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def _configure_extra_options(self, extra_options):
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self.extra_options = {
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"allocate_input_array": True,
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"allocate_output_array": True,
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"allocate_tmp_array": True,
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"sourcemodule_kwargs": {},
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"batch_along_flat_dims": True,
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}
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extra_opts = extra_options or {}
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self.extra_options.update(extra_opts)
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self.sourcemodule_kwargs = self.extra_options["sourcemodule_kwargs"]
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def _get_dimensions(self, shape, kernel):
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self.shape = shape
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self.data_ndim = self._check_dimensions(shape=shape, name="Data")
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self.kernel_ndim = self._check_dimensions(arr=kernel, name="Kernel")
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Nx = shape[-1]
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if self.data_ndim >= 2:
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Ny = shape[-2]
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else:
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Ny = 1
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if self.data_ndim >= 3:
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Nz = shape[-3]
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else:
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Nz = 1
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self.Nx = np.int32(Nx)
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self.Ny = np.int32(Ny)
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self.Nz = np.int32(Nz)
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def _determine_use_case(self, shape, kernel, axes):
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"""
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Determine the convolution use case from the input/kernel shape, and axes.
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"""
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self._get_dimensions(shape, kernel)
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if self.kernel_ndim > self.data_ndim:
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raise ValueError("Kernel dimensions cannot exceed data dimensions")
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data_ndim = self.data_ndim
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kernel_ndim = self.kernel_ndim
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self.kernel = kernel.astype("f")
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convol_infos = ConvolutionInfos()
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k = (data_ndim, kernel_ndim)
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if k not in convol_infos.use_cases:
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raise ValueError(
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"Cannot find a use case for data ndim = %d and kernel ndim = %d" % (data_ndim, kernel_ndim)
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)
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possible_use_cases = convol_infos.use_cases[k]
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# If some dimensions are "flat", make a batched convolution along them
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# Ex. data_dim = (1, Nx) -> batched 1D convolution
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if self.extra_options["batch_along_flat_dims"] and (1 in self.shape):
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axes = tuple([curr_dim for numels, curr_dim in zip(self.shape, range(len(self.shape))) if numels != 1])
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#
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self.use_case_name = None
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for uc_name, uc_params in possible_use_cases.items():
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if axes in convol_infos.allowed_axes[uc_name]:
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self.use_case_name = uc_name
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self.use_case_desc = uc_params["name"]
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self.use_case_kernels = uc_params["kernels"].copy()
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if self.use_case_name is None:
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raise ValueError(
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"Cannot find a use case for data ndim = %d, kernel ndim = %d and axes=%s"
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% (data_ndim, kernel_ndim, str(axes))
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)
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# TODO implement this use case
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if self.use_case_name == "batched_separable_2D_1D_3D":
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raise NotImplementedError("The use case %s is not implemented" % self.use_case_name)
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#
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self.axes = axes
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# Replace "axes=None" with an actual value (except for ND-ND)
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allowed_axes = convol_infos.allowed_axes[self.use_case_name]
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if len(allowed_axes) > 1:
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# The default choice might impact perfs
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self.axes = allowed_axes[0] or allowed_axes[1]
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self.separable = self.use_case_name.startswith("separable")
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self.batched = self.use_case_name.startswith("batched")
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def _allocate_memory(self, mode):
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self.mode = mode or "reflect"
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# The current implementation does not support kernel size bigger than data size,
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# except for mode="nearest"
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for i, dim_size in enumerate(self.shape):
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if min(self.kernel.shape) > dim_size and i in self.axes:
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print(
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"Warning: kernel support is too large for data dimension %d (%d). Forcing convolution mode to 'nearest'"
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% (i, dim_size)
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)
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self.mode = "nearest"
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#
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option_array_names = {
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"allocate_input_array": "data_in",
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"allocate_output_array": "data_out",
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"allocate_tmp_array": "data_tmp",
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}
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# Nonseparable transforms do not need tmp array
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if not (self.separable):
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self.extra_options["allocate_tmp_array"] = False
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# Allocate arrays
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for option_name, array_name in option_array_names.items():
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if self.extra_options[option_name]:
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value = self.cuda.allocate_array("value", self.shape, np.float32)
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else:
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value = None
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setattr(self, array_name, value)
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if isinstance(self.kernel, np.ndarray):
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self.d_kernel = self.cuda.to_device("d_kernel", self.kernel)
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else:
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if not (isinstance(self.kernel, self.cuda.array_class)):
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raise ValueError("kernel must be either numpy array or pycuda array")
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self.d_kernel = self.kernel
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self._old_input_ref = None
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self._old_output_ref = None
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self._c_modes_mapping = {
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"periodic": 2,
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"wrap": 2,
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"nearest": 1,
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"replicate": 1,
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"reflect": 0,
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"constant": 3,
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}
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mp = self._c_modes_mapping
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if self.mode.lower() not in mp:
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raise ValueError(
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"""
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Mode %s is not available. Available modes are:
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%s
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"""
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% (self.mode, str(mp.keys()))
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)
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if self.mode.lower() == "constant":
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raise NotImplementedError("mode='constant' is not implemented yet")
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self._c_conv_mode = mp[self.mode]
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def _init_kernels(self):
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if self.kernel_ndim > 1:
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if np.abs(np.diff(self.kernel.shape)).max() > 0:
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raise NotImplementedError("Non-separable convolution with non-square kernels is not implemented yet")
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# Compile source module
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compile_options = [str("-DUSED_CONV_MODE=%d" % self._c_conv_mode)]
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fname = get_cuda_srcfile("convolution.cu")
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nabu_cuda_dir = dirname(fname)
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include_dirs = [nabu_cuda_dir]
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self.sourcemodule_kwargs["options"] = compile_options
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self.sourcemodule_kwargs["include_dirs"] = include_dirs
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with open(fname) as fid:
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cuda_src = fid.read()
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self._module = SourceModule(cuda_src, **self.sourcemodule_kwargs)
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# Blocks, grid
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self._block_size = {1: (32, 1, 1), 2: (32, 32, 1), 3: (16, 8, 8)}[self.data_ndim] # TODO tune
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self._n_blocks = tuple([int(updiv(a, b)) for a, b in zip(self.shape[::-1], self._block_size)])
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# Prepare cuda kernel calls
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self._cudakernel_signature = {
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1: "PPPiiii",
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2: "PPPiiiii",
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3: "PPPiiiiii",
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}[self.kernel_ndim]
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self.cuda_kernels = {}
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211
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for axis, kern_name in enumerate(self.use_case_kernels):
|
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self.cuda_kernels[axis] = self._module.get_function(kern_name)
|
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self.cuda_kernels[axis].prepare(self._cudakernel_signature)
|
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|
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|
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# Cuda kernel arguments
|
216
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kernel_args = [
|
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self._n_blocks,
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self._block_size,
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None,
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None,
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self.d_kernel.gpudata,
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np.int32(self.kernel.shape[0]),
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self.Nx,
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self.Ny,
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self.Nz,
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]
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if self.kernel_ndim == 2:
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kernel_args.insert(5, np.int32(self.kernel.shape[1]))
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if self.kernel_ndim == 3:
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kernel_args.insert(5, np.int32(self.kernel.shape[2]))
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kernel_args.insert(6, np.int32(self.kernel.shape[1]))
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self.kernel_args = tuple(kernel_args)
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# If self.data_tmp is allocated, separable transforms can be performed
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# by a series of batched transforms, without any copy, by swapping refs.
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self.swap_pattern = None
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if self.separable:
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if self.data_tmp is not None:
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self.swap_pattern = {
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2: [("data_in", "data_tmp"), ("data_tmp", "data_out")],
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3: [
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241
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("data_in", "data_out"),
|
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("data_out", "data_tmp"),
|
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("data_tmp", "data_out"),
|
244
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],
|
245
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}
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246
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else:
|
247
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raise NotImplementedError("For now, data_tmp has to be allocated")
|
248
|
-
|
249
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def _get_swapped_arrays(self, i):
|
250
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-
"""
|
251
|
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Get the input and output arrays to use when using a "swap pattern".
|
252
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Swapping refs enables to avoid copies between temp. array and output.
|
253
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For example, a separable 2D->1D convolution on 2D data reads:
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data_tmp = convol(data_input, kernel, axis=1) # step i=0
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data_out = convol(data_tmp, kernel, axis=0) # step i=1
|
256
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-
|
257
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:param i: current step number of the separable convolution
|
258
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-
"""
|
259
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-
n_batchs = len(self.axes)
|
260
|
-
in_ref, out_ref = self.swap_pattern[n_batchs][i]
|
261
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d_in = getattr(self, in_ref)
|
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d_out = getattr(self, out_ref)
|
263
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-
return d_in, d_out
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|
265
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def _configure_kernel_args(self, cuda_kernel_args, input_ref, output_ref):
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266
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# TODO more elegant
|
267
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if isinstance(input_ref, self.cuda.array_class):
|
268
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input_ref = input_ref.gpudata
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if isinstance(output_ref, self.cuda.array_class):
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output_ref = output_ref.gpudata
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if input_ref is not None or output_ref is not None:
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cuda_kernel_args = list(cuda_kernel_args)
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273
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if input_ref is not None:
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-
cuda_kernel_args[2] = input_ref
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275
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-
if output_ref is not None:
|
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cuda_kernel_args[3] = output_ref
|
277
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-
cuda_kernel_args = tuple(cuda_kernel_args)
|
278
|
-
return cuda_kernel_args
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279
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-
|
280
|
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@staticmethod
|
281
|
-
def _check_dimensions(arr=None, shape=None, name="", dim_min=1, dim_max=3):
|
282
|
-
if shape is not None:
|
283
|
-
ndim = len(shape)
|
284
|
-
elif arr is not None:
|
285
|
-
ndim = arr.ndim
|
286
|
-
else:
|
287
|
-
raise ValueError("Please provide either arr= or shape=")
|
288
|
-
if ndim < dim_min or ndim > dim_max:
|
289
|
-
raise ValueError("%s dimensions should be between %d and %d" % (name, dim_min, dim_max))
|
290
|
-
return ndim
|
291
|
-
|
292
|
-
def _check_array(self, arr):
|
293
|
-
if not (isinstance(arr, self.cuda.array_class) or isinstance(arr, np.ndarray)):
|
294
|
-
raise TypeError("Expected either pycuda.gpuarray or numpy.ndarray")
|
295
|
-
if arr.dtype != np.float32:
|
296
|
-
raise TypeError("Data must be float32")
|
297
|
-
if arr.shape != self.shape:
|
298
|
-
raise ValueError("Expected data shape = %s" % str(self.shape))
|
299
|
-
|
300
|
-
def _set_arrays(self, array, output=None):
|
301
|
-
# Either copy H->D or update references.
|
302
|
-
if isinstance(array, np.ndarray):
|
303
|
-
self.data_in[:] = array[:]
|
304
|
-
else:
|
305
|
-
self._old_input_ref = self.data_in
|
306
|
-
self.data_in = array
|
307
|
-
data_in_ref = self.data_in
|
308
|
-
if output is not None:
|
309
|
-
if not (isinstance(output, np.ndarray)):
|
310
|
-
self._old_output_ref = self.data_out
|
311
|
-
self.data_out = output
|
312
|
-
# Update Cuda kernel arguments with new array references
|
313
|
-
self.kernel_args = self._configure_kernel_args(self.kernel_args, data_in_ref, self.data_out)
|
314
|
-
|
315
|
-
def _separable_convolution(self):
|
316
|
-
assert len(self.axes) == len(self.use_case_kernels)
|
317
|
-
# Separable: one kernel call per data dimension
|
318
|
-
for i, axis in enumerate(self.axes):
|
319
|
-
in_ref, out_ref = self._get_swapped_arrays(i)
|
320
|
-
self._batched_convolution(axis, input_ref=in_ref, output_ref=out_ref)
|
321
|
-
|
322
|
-
def _batched_convolution(self, axis, input_ref=None, output_ref=None):
|
323
|
-
# Batched: one kernel call in total
|
324
|
-
cuda_kernel = self.cuda_kernels[axis]
|
325
|
-
cuda_kernel_args = self._configure_kernel_args(self.kernel_args, input_ref, output_ref)
|
326
|
-
ev = cuda_kernel.prepared_call(*cuda_kernel_args)
|
327
|
-
|
328
|
-
def _nd_convolution(self):
|
329
|
-
assert len(self.use_case_kernels) == 1
|
330
|
-
cuda_kernel = self._module.get_function(self.use_case_kernels[0])
|
331
|
-
ev = cuda_kernel.prepared_call(*self.kernel_args)
|
332
|
-
|
333
|
-
def _recover_arrays_references(self):
|
334
|
-
if self._old_input_ref is not None:
|
335
|
-
self.data_in = self._old_input_ref
|
336
|
-
self._old_input_ref = None
|
337
|
-
if self._old_output_ref is not None:
|
338
|
-
self.data_out = self._old_output_ref
|
339
|
-
self._old_output_ref = None
|
340
|
-
self.kernel_args = self._configure_kernel_args(self.kernel_args, self.data_in, self.data_out)
|
341
|
-
|
342
|
-
def _get_output(self, output):
|
343
|
-
if output is None:
|
344
|
-
res = self.data_out.get()
|
345
|
-
else:
|
346
|
-
res = output
|
347
|
-
if isinstance(output, np.ndarray):
|
348
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output[:] = self.data_out[:]
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self._recover_arrays_references()
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def convolve(self, array, output=None):
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"""
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Convolve an array with the class kernel.
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:param array: Input array. Can be numpy.ndarray or pycuda.gpuarray.GPUArray.
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:param output: Output array. Can be numpy.ndarray or pycuda.gpuarray.GPUArray.
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self._check_array(array)
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self._set_arrays(array, output=output)
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self._separable_convolution()
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assert len(self.axes) == 1
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self._batched_convolution(self.axes[0])
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# else: ND-ND convol
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else:
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# ND-ND convol
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self._nd_convolution()
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res = self._get_output(output)
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return res
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__call__ = convolve
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import numpy as np
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from ..utils import BaseClassError
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class _BaseFFT:
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"""
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A base class for FFTs.
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"""
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implem = "none"
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ProcessingCls = BaseClassError
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def __init__(self, shape, dtype, r2c=True, axes=None, normalize="rescale", **backend_options):
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"""
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Base class for Fast Fourier Transform (FFT).
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Parameters
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----------
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shape: list of int
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Shape of the input data
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dtype: str or numpy.dtype
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Data type of the input data
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r2c: bool, optional
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Whether to use real-to-complex transform for real-valued input. Default is True.
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axes: list of int, optional
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Axes along which FFT is computed.
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* For 2D transform: axes=(1,0)
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* For batched 1D transform of 2D image: axes=(-1,)
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normalize: str, optional
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Whether to normalize FFT and IFFT. Possible values are:
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* "rescale": in this case, Fourier data is divided by "N"
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before IFFT, so that IFFT(FFT(data)) = data.
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This corresponds to numpy norm=None i.e norm="backward".
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* "ortho": in this case, FFT and IFFT are adjoint of eachother,
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the transform is unitary. Both FFT and IFFT are scaled with 1/sqrt(N).
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* "none": no normalizatio is done : IFFT(FFT(data)) = data*N
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Other parameters
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-----------------
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backend_options: dict, optional
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Parameters to pass to CudaProcessing or OpenCLProcessing class.
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"""
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self._init_backend(backend_options)
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self._set_dtypes(dtype, r2c)
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self._set_shape_and_axes(shape, axes)
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self._configure_batched_transform()
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self._configure_normalization(normalize)
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self._compute_fft_plans()
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def _init_backend(self, backend_options):
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self.processing = self.ProcessingCls(**backend_options)
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def _set_dtypes(self, dtype, r2c):
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self.dtype = np.dtype(dtype)
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dtypes_mapping = {
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np.dtype("float32"): np.complex64,
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np.dtype("float64"): np.complex128,
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np.dtype("complex64"): np.complex64,
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np.dtype("complex128"): np.complex128,
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}
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if self.dtype not in dtypes_mapping:
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raise ValueError("Invalid input data type: got %s" % self.dtype)
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self.dtype_out = dtypes_mapping[self.dtype]
|
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self.r2c = r2c
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def _set_shape_and_axes(self, shape, axes):
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# Input shape
|
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|
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if np.isscalar(shape):
|
69
|
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shape = (shape,)
|
70
|
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self.shape = shape
|
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|
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# Axes
|
72
|
-
default_axes = tuple(range(len(self.shape)))
|
73
|
-
if axes is None:
|
74
|
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self.axes = default_axes
|
75
|
-
else:
|
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|
-
self.axes = tuple(np.array(default_axes)[np.array(axes)])
|
77
|
-
# Output shape
|
78
|
-
shape_out = self.shape
|
79
|
-
if self.r2c:
|
80
|
-
reduced_dim = self.axes[-1] if self.axes is not None else -1
|
81
|
-
shape_out = list(shape_out)
|
82
|
-
shape_out[reduced_dim] = shape_out[reduced_dim] // 2 + 1
|
83
|
-
shape_out = tuple(shape_out)
|
84
|
-
self.shape_out = shape_out
|
85
|
-
|
86
|
-
def _configure_batched_transform(self):
|
87
|
-
pass
|
88
|
-
|
89
|
-
def _configure_normalization(self, normalize):
|
90
|
-
pass
|
91
|
-
|
92
|
-
def _compute_fft_plans(self):
|
93
|
-
pass
|
94
|
-
|
95
|
-
|
96
|
-
class _BaseVKFFT(_BaseFFT):
|
97
|
-
"""
|
98
|
-
FFT using VKFFT backend
|
99
|
-
"""
|
100
|
-
|
101
|
-
implem = "vkfft"
|
102
|
-
backend = "none"
|
103
|
-
ProcessingCls = BaseClassError
|
104
|
-
vkffs_cls = BaseClassError
|
105
|
-
|
106
|
-
def _configure_batched_transform(self):
|
107
|
-
if self.axes is not None and len(self.shape) == len(self.axes):
|
108
|
-
self.axes = None
|
109
|
-
return
|
110
|
-
if self.r2c:
|
111
|
-
# batched Real-to-complex transforms are supported only along fast axes
|
112
|
-
if not (is_fast_axes(len(self.shape), self.axes)):
|
113
|
-
raise ValueError("For %dD R2C, only batched transforms along fast axes are allowed" % (len(self.shape)))
|
114
|
-
self._vkfft_ndim = len(self.axes)
|
115
|
-
self.axes = None # vkfft still can do a batched transform by providing dim=XX, axes=None
|
116
|
-
|
117
|
-
def _configure_normalization(self, normalize):
|
118
|
-
self.normalize = normalize
|
119
|
-
self._vkfft_norm = {
|
120
|
-
"rescale": 1,
|
121
|
-
"backward": 1,
|
122
|
-
"ortho": "ortho",
|
123
|
-
"none": 0,
|
124
|
-
}.get(self.normalize, 1)
|
125
|
-
|
126
|
-
def _set_shape_and_axes(self, shape, axes):
|
127
|
-
super()._set_shape_and_axes(shape, axes)
|
128
|
-
self._vkfft_ndim = None
|
129
|
-
|
130
|
-
def _compute_fft_plans(self):
|
131
|
-
self._vkfft_plan = self.vkffs_cls(
|
132
|
-
self.shape,
|
133
|
-
self.dtype,
|
134
|
-
ndim=self._vkfft_ndim,
|
135
|
-
inplace=False,
|
136
|
-
norm=self._vkfft_norm,
|
137
|
-
r2c=self.r2c,
|
138
|
-
dct=False,
|
139
|
-
axes=self.axes,
|
140
|
-
strides=None,
|
141
|
-
**self._vkfft_other_init_kwargs,
|
142
|
-
)
|
143
|
-
|
144
|
-
def fft(self, array, output=None):
|
145
|
-
if output is None:
|
146
|
-
output = self.output_fft = self.processing.allocate_array(
|
147
|
-
"output_fft", self.shape_out, dtype=self.dtype_out
|
148
|
-
)
|
149
|
-
return self._vkfft_plan.fft(array, dest=output)
|
150
|
-
|
151
|
-
def ifft(self, array, output=None):
|
152
|
-
if output is None:
|
153
|
-
output = self.output_ifft = self.processing.allocate_array("output_ifft", self.shape, dtype=self.dtype)
|
154
|
-
return self._vkfft_plan.ifft(array, dest=output)
|
155
|
-
|
156
|
-
|
157
|
-
def is_fast_axes(ndim, axes):
|
158
|
-
"""
|
159
|
-
Return true if "axes" are the fast dimensions
|
160
|
-
"""
|
161
|
-
all_axes = list(range(ndim))
|
162
|
-
axes = sorted([ax + ndim if ax < 0 else ax for ax in axes]) # transform "-1" to an actual axis index (1 for 2D)
|
163
|
-
return all_axes[-len(axes) :] == axes
|