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/reconstruction/tests/test_sino_normalization.py +0 -85
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- 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
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- 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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import numpy as np
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import pycuda.driver as cuda
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from ..utils import updiv, get_cuda_srcfile
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from ..cuda.utils import copy_array, check_textures_availability
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from ..cuda.processing import CudaProcessing
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from .filtering_cuda import CudaSinoFilter
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class CudaBackprojector(BackprojectorBase):
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kernel_filename = "backproj.cu"
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backend_processing_class = CudaProcessing
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SinoFilterClass = CudaSinoFilter
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SinoMultClass = CudaSinoMult
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def _check_textures_availability(self):
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{
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"file_name": get_cuda_srcfile(self.kernel_filename),
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"kernel_signature": self._get_kernel_signature(),
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"texture_name": "tex_projections",
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self._d_sino = self._processing.allocate_array("_d_sino", self.sino_shape)
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self.gpu_projector.prepare(self._kernel_options["kernel_signature"], [self.texref_proj])
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self.gpu_projector.prepare(self._kernel_options["kernel_signature"], [])
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self.gpu_projector = CudaKernel(
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self._kernel_options["kernel_name"],
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filename=self._kernel_options["file_name"],
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options=self._kernel_options["sourcemodule_options"],
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)
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if self.halftomo and self.rot_center < self.dwidth:
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self.sino_mult = CudaSinoMult(self.sino_shape, self.rot_center, ctx=self._processing.ctx)
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copy_array(self._d_sino_cua, sino, check=do_checks)
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# COMPAT.
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Backprojector = CudaBackprojector
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class PolarBackprojector(Backprojector):
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Cuda Backprojector with output in polar coordinates.
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"""
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# patch parent method: force slice_shape to (n_angles, n_x)
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def _set_angles(self, angles, n_angles):
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Backprojector._set_angles(self, angles, n_angles)
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# patch parent method:
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def _set_slice_roi(self, slice_roi):
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raise ValueError("slice_roi is not supported with this class")
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Backprojector._set_slice_roi(self, slice_roi)
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# patch parent method: don't do the 4X compute-workload optimization for this kernel
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def _get_kernel_options(self):
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Backprojector._get_kernel_options(self)
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block = self._kernel_options["block"]
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self._kernel_options["grid"] = (updiv(self.n_x, block[0]), updiv(self.n_y, block[1]))
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def _compile_kernels(self):
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self.n_y = self.n_angles
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Backprojector._compile_kernels(self)
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self.n_y = n_y
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import numpy as np
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from ..utils import updiv, nextpow2, convert_index, deprecation_warning
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from ..processing.processing_base import ProcessingBase
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from .filtering import SinoFilter
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from .sinogram import SinoMult
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from .sinogram import get_extended_sinogram_width
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class BackprojectorBase:
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Base class for backprojectors.
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"""
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backend = "numpy"
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default_extra_options = {
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"clip_outer_circle": False,
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"scale_factor": None,
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"filter_cutoff": 1.0,
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}
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kernel_filename = None
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SinoFilterClass = SinoFilter
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SinoMultClass = SinoMult
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_sino_filter_other_options = {}
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def __init__(
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self,
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sino_shape,
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slice_shape=None,
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angles=None,
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rot_center=None,
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padding_mode=None,
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halftomo=False,
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filter_name=None,
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slice_roi=None,
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scale_factor=None,
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extra_options=None,
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backend_options=None,
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):
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"""
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Initialize a Backprojector.
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Parameters
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-----------
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sino_shape: tuple
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Shape of the sinogram, in the form `(n_angles, detector_width)`
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(for backprojecting one sinogram) or `(n_sinos, n_angles, detector_width)`.
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slice_shape: int or tuple, optional
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Shape of the slice. By default, the slice shape is (n_x, n_x) where
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`n_x = detector_width`
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angles: array-like, optional
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Rotation anles in radians.
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By default, angles are equispaced between [0, pi[.
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rot_center: float, optional
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Rotation axis position. Default is `(detector_width - 1)/2.0`
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padding_mode: str, optional
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Padding mode when filtering the sinogram. Can be "zeros" (default) or "edges".
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filter_name: str, optional
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Name of the filter for filtered-backprojection.
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slice_roi: tuple, optional.
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Whether to backproject in a restricted area.
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If set, it must be in the form (start_x, end_x, start_y, end_y).
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`end_x` and `end_y` are non inclusive ! For example if the detector has
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2048 pixels horizontally, then you can choose `start_x=0` and `end_x=2048`.
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If one of the value is set to None, it is replaced with a default value
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(0 for start, n_x and n_y for end)
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scale_factor: float, optional
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Scaling factor for backprojection.
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For example, to get the linear absorption coefficient in 1/cm,
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this factor has to be set as the pixel size in cm.
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DEPRECATED - please use this parameter in "extra_options"
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Advanced extra options.
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See the "Extra options" section for more information.
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backend_options: dict, optional
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OpenCL/Cuda options passed to the OpenCLProcessing or CudaProcessing class.
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Other parameters
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-----------------
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extra_options: dict, optional
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Dictionary with a set of advanced options. The default are the following:
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Padding mode when filtering the sinogram. Can be "zeros" or "edges".
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DEPRECATED - please use "padding_mode" directly in parameters.
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Whether to set a correction for the rotation axis.
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If set, this should be an array with as many elements as the number
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of angles. This is useful when there is an horizontal displacement
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of the rotation axis.
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Whether to "center" the slice on the rotation axis position.
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If set to True, then the reconstructed region is centered on the rotation axis.
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- scale_factor: float
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Scaling factor for backprojection.
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For example, to get the linear absorption coefficient in 1/cm,
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this factor has to be set as the pixel size in cm.
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Whether to set to zero the pixels outside the reconstruction mask
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Cut-off frequency usef for Fourier filter. Default is 1.0
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"""
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self._processing = self.backend_processing_class(**(backend_options or {}))
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self._configure_extra_options(scale_factor, padding_mode, extra_options=extra_options)
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self._check_textures_availability()
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self._init_geometry(sino_shape, slice_shape, angles, rot_center, halftomo, slice_roi)
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self._init_filter(filter_name)
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self._allocate_memory()
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self._compute_angles()
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self._compile_kernels()
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def _configure_extra_options(self, scale_factor, padding_mode, extra_options=None):
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extra_options = extra_options or {}
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# compat.
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scale_factor = None
|
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if scale_factor is not None:
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deprecation_warning(
|
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"Please use the parameter 'scale_factor' in the 'extra_options' dict",
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do_print=True,
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func_name="fbp_scale_factor",
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)
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scale_factor = extra_options.get("scale_factor", None) or scale_factor or 1.0
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#
|
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if "padding_mode" in extra_options:
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deprecation_warning(
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"Please use 'padding_mode' directly in Backprojector arguments, not in 'extra_options'",
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do_print=True,
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func_name="fbp_padding_mode",
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)
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#
|
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self._backproj_scale_factor = scale_factor
|
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self._axis_array = None
|
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self.extra_options = self.default_extra_options.copy()
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self.extra_options.update(extra_options)
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self.padding_mode = padding_mode or self.extra_options["padding_mode"] or self.default_padding_mode
|
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self._axis_array = self.extra_options["axis_correction"]
|
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|
143
|
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def _init_geometry(self, sino_shape, slice_shape, angles, rot_center, halftomo, slice_roi):
|
144
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if slice_shape is not None and slice_roi is not None:
|
145
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raise ValueError("slice_shape and slice_roi cannot be used together")
|
146
|
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self.sino_shape = sino_shape
|
147
|
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if len(sino_shape) == 2:
|
148
|
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n_angles, dwidth = sino_shape
|
149
|
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else:
|
150
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raise ValueError("Expected 2D sinogram")
|
151
|
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self.dwidth = dwidth
|
152
|
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self.halftomo = halftomo
|
153
|
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if rot_center is None:
|
154
|
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if halftomo:
|
155
|
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raise ValueError("Need to know 'rot_center' when using halftomo")
|
156
|
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rot_center = (self.dwidth - 1) / 2.0
|
157
|
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self.rot_center = rot_center
|
158
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self._set_slice_shape(slice_shape)
|
159
|
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self.axis_pos = self.rot_center
|
160
|
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self._set_angles(angles, n_angles)
|
161
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self._set_slice_roi(slice_roi)
|
162
|
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#
|
163
|
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# offset = start - move
|
164
|
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# move = 0 if not(centered_axis) else start + (n-1)/2. - c
|
165
|
-
if self.extra_options["centered_axis"]:
|
166
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self.offsets = {
|
167
|
-
"x": self.rot_center - (self.n_x - 1) / 2.0,
|
168
|
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"y": self.rot_center - (self.n_y - 1) / 2.0,
|
169
|
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}
|
170
|
-
#
|
171
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self._set_axis_corr()
|
172
|
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|
173
|
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def _set_slice_shape(self, slice_shape):
|
174
|
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if not (self.halftomo):
|
175
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n_x = n_y = self.dwidth
|
176
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else:
|
177
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n_x = n_y = get_extended_sinogram_width(self.dwidth, self.rot_center)
|
178
|
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if slice_shape is not None:
|
179
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if np.isscalar(slice_shape):
|
180
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slice_shape = (slice_shape, slice_shape)
|
181
|
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n_y, n_x = slice_shape
|
182
|
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self.n_x = n_x
|
183
|
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self.n_y = n_y
|
184
|
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self.slice_shape = (n_y, n_x)
|
185
|
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|
186
|
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def _set_angles(self, angles, n_angles):
|
187
|
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self.n_angles = n_angles
|
188
|
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if angles is None:
|
189
|
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angles = n_angles
|
190
|
-
if np.isscalar(angles):
|
191
|
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end_angle = np.pi if not (self.halftomo) else 2 * np.pi
|
192
|
-
take_end_angle = self.halftomo
|
193
|
-
angles = np.linspace(0, end_angle, angles, take_end_angle)
|
194
|
-
else:
|
195
|
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assert len(angles) == self.n_angles, "expected %d angles but got %d" % (len(angles), self.n_angles)
|
196
|
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self.angles = angles
|
197
|
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|
198
|
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def _set_slice_roi(self, slice_roi):
|
199
|
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self.offsets = {"x": 0, "y": 0}
|
200
|
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self.slice_roi = slice_roi
|
201
|
-
if slice_roi is None:
|
202
|
-
return
|
203
|
-
start_x, end_x, start_y, end_y = slice_roi
|
204
|
-
# convert negative indices
|
205
|
-
start_x = convert_index(start_x, self.n_x, 0)
|
206
|
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start_y = convert_index(start_y, self.n_y, 0)
|
207
|
-
end_x = convert_index(end_x, self.n_x, self.n_x)
|
208
|
-
end_y = convert_index(end_y, self.n_y, self.n_y)
|
209
|
-
self.slice_shape = (end_y - start_y, end_x - start_x)
|
210
|
-
self.n_x = self.slice_shape[-1]
|
211
|
-
self.n_y = self.slice_shape[-2]
|
212
|
-
self.offsets = {"x": start_x, "y": start_y}
|
213
|
-
|
214
|
-
def _allocate_memory(self):
|
215
|
-
# 1D textures are not supported in pyopencl
|
216
|
-
self.h_msin = np.zeros((1, self.n_angles), "f")
|
217
|
-
self.h_cos = np.zeros((1, self.n_angles), "f")
|
218
|
-
# self._d_sino = self._processing.allocate_array("d_sino", self.sino_shape, "f")
|
219
|
-
self._processing.init_arrays_to_none(["_d_slice", "d_sino"])
|
220
|
-
|
221
|
-
def _compute_angles(self):
|
222
|
-
self.h_cos[0] = np.cos(self.angles).astype("f")
|
223
|
-
self.h_msin[0] = (-np.sin(self.angles)).astype("f")
|
224
|
-
self._d_msin = self._processing.set_array("d_msin", self.h_msin[0])
|
225
|
-
self._d_cos = self._processing.set_array("d_cos", self.h_cos[0])
|
226
|
-
if self._axis_correction is not None:
|
227
|
-
self._d_axcorr = self._processing._set_array("d_axcorr", self._axis_correction)
|
228
|
-
|
229
|
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def _set_axis_corr(self):
|
230
|
-
axcorr = self.extra_options["axis_correction"]
|
231
|
-
self._axis_correction = axcorr
|
232
|
-
if axcorr is None:
|
233
|
-
return
|
234
|
-
if len(axcorr) != self.n_angles:
|
235
|
-
raise ValueError("Expected %d angles but got %d" % (self.n_angles, len(axcorr)))
|
236
|
-
self._axis_correction = np.zeros((1, self.n_angles), dtype=np.float32)
|
237
|
-
self._axis_correction[0, :] = axcorr[:] # pylint: disable=E1136
|
238
|
-
|
239
|
-
def _init_filter(self, filter_name):
|
240
|
-
self.filter_name = filter_name
|
241
|
-
if filter_name in ["None", "none"]:
|
242
|
-
self.sino_filter = None
|
243
|
-
return
|
244
|
-
sinofilter_other_kwargs = {}
|
245
|
-
if self.backend != "numpy":
|
246
|
-
sinofilter_other_kwargs["%s_options" % self.backend] = {"ctx": self._processing.ctx}
|
247
|
-
self.sino_filter = self.SinoFilterClass(
|
248
|
-
self.sino_shape,
|
249
|
-
filter_name=self.filter_name,
|
250
|
-
padding_mode=self.padding_mode,
|
251
|
-
extra_options={"cutoff": self.extra_options.get("filter_cutoff", 1.0)},
|
252
|
-
**sinofilter_other_kwargs,
|
253
|
-
)
|
254
|
-
if self.halftomo:
|
255
|
-
# When doing half-tomography, each projections is seen "twice".
|
256
|
-
# SinoFilter normalizes with pi/n_angles, but in half-tomography here n_angles is somehow halved.
|
257
|
-
# TODO it should even be "n_turns", where n_turns can be computed from the angles
|
258
|
-
self.sino_filter.set_filter(self.sino_filter.filter_f * (self.n_angles / np.pi * 2))
|
259
|
-
|
260
|
-
def reset_rot_center(self, rot_center):
|
261
|
-
"""
|
262
|
-
Define a new center of rotation for the current backprojector.
|
263
|
-
"""
|
264
|
-
self.rot_center = rot_center
|
265
|
-
self.axis_pos = rot_center
|
266
|
-
# See kernels signature of backproj.cu and backproj.cl.
|
267
|
-
# The ifdef makes things a bit more complicated
|
268
|
-
proj_arg_idx = 4
|
269
|
-
if self.backend == "cuda" and self._use_textures:
|
270
|
-
proj_arg_idx = 3
|
271
|
-
self.kern_proj_args[proj_arg_idx] = rot_center
|
272
|
-
if self.extra_options["centered_axis"]:
|
273
|
-
self.offsets = {
|
274
|
-
"x": self.rot_center - (self.n_x - 1) / 2.0,
|
275
|
-
"y": self.rot_center - (self.n_y - 1) / 2.0,
|
276
|
-
}
|
277
|
-
self.kern_proj_args[proj_arg_idx + 3] = self.offsets["x"]
|
278
|
-
self.kern_proj_args[proj_arg_idx + 4] = self.offsets["y"]
|
279
|
-
|
280
|
-
# Try to factorize some code between Cuda and OpenCL
|
281
|
-
# Not ideal, as cuda uses "grid" = n_blocks_launched,
|
282
|
-
# while OpenCL uses "global_size" = n_threads_launched
|
283
|
-
def _get_kernel_options(self):
|
284
|
-
sourcemodule_options = []
|
285
|
-
# We use blocks of 16*16 (see why in kernel doc), and one thread
|
286
|
-
# handles 2 pixels per dimension.
|
287
|
-
block = (16, 16, 1)
|
288
|
-
# The Cuda kernel is optimized for 16x16 threads blocks
|
289
|
-
# If one of the dimensions is smaller than 16, it has to be addapted
|
290
|
-
if self.n_x < 16 or self.n_y < 16:
|
291
|
-
tpb_x = min(int(nextpow2(self.n_x)), 16)
|
292
|
-
tpb_y = min(int(nextpow2(self.n_y)), 16)
|
293
|
-
block = (tpb_x, tpb_y, 1)
|
294
|
-
sourcemodule_options.append("-DSHARED_SIZE=%d" % (tpb_x * tpb_y))
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grid = (updiv(updiv(self.n_x, block[0]), 2), updiv(updiv(self.n_y, block[1]), 2))
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if self.extra_options["clip_outer_circle"]:
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sourcemodule_options.append("-DCLIP_OUTER_CIRCLE")
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shared_size = int(np.prod(block)) * 2
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if self._axis_correction is not None:
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sourcemodule_options.append("-DDO_AXIS_CORRECTION")
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shared_size += int(np.prod(block))
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shared_size *= 4 # sizeof(float32)
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self._kernel_options = {
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"kernel_name": self.kernel_name,
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"sourcemodule_options": sourcemodule_options,
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"grid": grid,
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"block": block,
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"shared_size": shared_size,
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}
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def _prepare_kernel_args(self):
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self._get_kernel_options()
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self.kern_proj_args = [
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None, # output d_slice holder
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None, # placeholder for sino (OpenCL or Cuda+no-texture)
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np.int32(self.n_angles),
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np.int32(self.dwidth),
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np.float32(self.axis_pos),
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np.int32(self.n_x),
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np.int32(self.n_y),
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np.float32(self.offsets["x"]),
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np.float32(self.offsets["y"]),
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self._d_cos,
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self._d_msin,
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np.float32(self._backproj_scale_factor),
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]
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if self._axis_correction is not None:
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self.kern_proj_args.insert(-1, self._d_axcorr)
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self.kern_proj_kwargs = {
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"grid": self._kernel_options["grid"],
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|
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"block": self._kernel_options["block"],
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}
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|
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def _set_output(self, output, check=False):
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self._output_is_ndarray = isinstance(output, np.ndarray)
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|
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if output is None or self._output_is_ndarray:
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self._processing.allocate_array("_d_slice", self.slice_shape, dtype=np.float32)
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return self._processing._d_slice # pylint: disable=E1101
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if check:
|
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assert output.dtype == np.float32
|
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|
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assert output.shape == self.slice_shape, "Expected output shape %s but got %s" % (
|
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self.slice_shape,
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output.shape,
|
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|
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)
|
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|
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return output
|
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|
-
|
347
|
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def _set_kernel_slice_arg(self, d_slice):
|
348
|
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self.kern_proj_args[0] = d_slice
|
349
|
-
|
350
|
-
def backproj(self, sino, output=None, do_checks=True):
|
351
|
-
if self.halftomo and self.rot_center < self.dwidth:
|
352
|
-
self.sino_mult.prepare_sino(sino)
|
353
|
-
self._transfer_to_texture(sino)
|
354
|
-
d_slice = self._set_output(output, check=do_checks)
|
355
|
-
self._set_kernel_slice_arg(d_slice)
|
356
|
-
self.gpu_projector(*self.kern_proj_args, **self.kern_proj_kwargs)
|
357
|
-
if output is not None and not (self._output_is_ndarray):
|
358
|
-
return output
|
359
|
-
else:
|
360
|
-
return self._processing._d_slice.get(ary=output)
|
361
|
-
|
362
|
-
def filtered_backprojection(self, sino, output=None):
|
363
|
-
#
|
364
|
-
if isinstance(sino, self._processing.array_class):
|
365
|
-
d_sino = sino
|
366
|
-
else:
|
367
|
-
d_sino = self._processing.to_device("d_sino", sino)
|
368
|
-
#
|
369
|
-
if self.sino_filter is not None:
|
370
|
-
filt_kwargs = {}
|
371
|
-
# if a new device array was allocated for sinogram, then the filtering can overwrite it,
|
372
|
-
# since it won't affect user argument
|
373
|
-
if id(d_sino) != id(sino):
|
374
|
-
filt_kwargs = {"output": d_sino}
|
375
|
-
#
|
376
|
-
sino_to_backproject = self.sino_filter(d_sino, **filt_kwargs)
|
377
|
-
else:
|
378
|
-
sino_to_backproject = d_sino
|
379
|
-
return self.backproj(sino_to_backproject, output=output)
|
380
|
-
|
381
|
-
fbp = filtered_backprojection # shorthand
|
382
|
-
|
383
|
-
def __repr__(self):
|
384
|
-
res = "%s(sino_shape=%s, slice_shape=%s, rot_center=%.2f, halftomo=%s)" % (
|
385
|
-
self.__class__.__name__,
|
386
|
-
str(self.sino_shape),
|
387
|
-
str(self.slice_shape),
|
388
|
-
self.rot_center,
|
389
|
-
self.halftomo,
|
390
|
-
)
|
391
|
-
return res
|
@@ -1,78 +0,0 @@
|
|
1
|
-
import pyopencl as cl
|
2
|
-
from ..utils import get_opencl_srcfile
|
3
|
-
from ..opencl.processing import OpenCLProcessing
|
4
|
-
from ..opencl.kernel import OpenCLKernel
|
5
|
-
from ..opencl.utils import allocate_texture, check_textures_availability, copy_to_texture
|
6
|
-
from .filtering_opencl import OpenCLSinoFilter
|
7
|
-
from .sinogram_opencl import OpenCLSinoMult
|
8
|
-
from .fbp_base import BackprojectorBase
|
9
|
-
|
10
|
-
|
11
|
-
class OpenCLBackprojector(BackprojectorBase):
|
12
|
-
default_extra_options = {**BackprojectorBase.default_extra_options, "use_textures": True}
|
13
|
-
backend = "opencl"
|
14
|
-
kernel_filename = "backproj.cl"
|
15
|
-
backend_processing_class = OpenCLProcessing
|
16
|
-
SinoFilterClass = OpenCLSinoFilter
|
17
|
-
SinoMultClass = OpenCLSinoMult
|
18
|
-
|
19
|
-
def _check_textures_availability(self):
|
20
|
-
self._use_textures = self.extra_options.get("use_textures", True) and check_textures_availability(
|
21
|
-
self._processing.ctx
|
22
|
-
)
|
23
|
-
|
24
|
-
def _get_kernel_options(self):
|
25
|
-
super()._get_kernel_options()
|
26
|
-
self._kernel_options.update(
|
27
|
-
{
|
28
|
-
"file_name": get_opencl_srcfile(self.kernel_filename),
|
29
|
-
}
|
30
|
-
)
|
31
|
-
|
32
|
-
def _prepare_kernel_args(self):
|
33
|
-
super()._prepare_kernel_args()
|
34
|
-
block = self.kern_proj_kwargs.pop("block")
|
35
|
-
local_size = block
|
36
|
-
grid = self.kern_proj_kwargs.pop("grid")
|
37
|
-
global_size = (grid[0] * block[0], grid[1] * block[1])
|
38
|
-
# global_size = (updiv(self.n_x, 2), updiv(self.n_y, 2))
|
39
|
-
self.kern_proj_args.insert(0, self._processing.queue) # OpenCLProcessing.__call__ expects first arg to be queue
|
40
|
-
self.kern_proj_kwargs.update(
|
41
|
-
{
|
42
|
-
"global_size": global_size,
|
43
|
-
"local_size": local_size,
|
44
|
-
}
|
45
|
-
)
|
46
|
-
|
47
|
-
def _prepare_textures(self):
|
48
|
-
if self._use_textures:
|
49
|
-
d_sino_ref = self.d_sino_tex = allocate_texture(self._processing.ctx, self.sino_shape)
|
50
|
-
self._kernel_options["sourcemodule_options"].append("-DUSE_TEXTURES")
|
51
|
-
else:
|
52
|
-
self._d_sino = self._processing.allocate_array("_d_sino", self.sino_shape)
|
53
|
-
d_sino_ref = self._d_sino.data
|
54
|
-
self.kern_proj_args[2] = d_sino_ref
|
55
|
-
|
56
|
-
def _compile_kernels(self):
|
57
|
-
self._prepare_kernel_args()
|
58
|
-
self._prepare_textures() # has to be done before compilation for OpenCL (to pass -DUSE_TEXTURES)
|
59
|
-
self.kern_proj_args.append(cl.LocalMemory(self._kernel_options["shared_size"]))
|
60
|
-
self.gpu_projector = OpenCLKernel(
|
61
|
-
self._kernel_options["kernel_name"],
|
62
|
-
self._processing.ctx,
|
63
|
-
filename=self._kernel_options["file_name"],
|
64
|
-
options=self._kernel_options["sourcemodule_options"],
|
65
|
-
)
|
66
|
-
if self.halftomo and self.rot_center < self.dwidth:
|
67
|
-
self.sino_mult = OpenCLSinoMult(self.sino_shape, self.rot_center, ctx=self._processing.ctx)
|
68
|
-
|
69
|
-
def _transfer_to_texture(self, sino, do_checks=True):
|
70
|
-
if self._use_textures:
|
71
|
-
return copy_to_texture(self._processing.queue, self.d_sino_tex, sino)
|
72
|
-
else:
|
73
|
-
if id(self._d_sino) == id(sino):
|
74
|
-
return
|
75
|
-
return cl.enqueue_copy(self._processing.queue, self._d_sino.data, sino.data)
|
76
|
-
|
77
|
-
def _set_kernel_slice_arg(self, d_slice):
|
78
|
-
self.kern_proj_args[1] = d_slice
|