nabu 2024.1.0rc3__py3-none-any.whl → 2024.1.1__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.
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/doc/conf.py +137 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/doc/create_conf_doc.py +38 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/doc/get_mathjax.py +34 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/__init__.py +17 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/__init__.py +0 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/bootstrap.py +88 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/bootstrap_stitching.py +69 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/cast_volume.py +272 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/cli_configs.py +626 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/compare_volumes.py +94 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/composite_cor.py +144 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/correct_rot.py +70 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/create_distortion_map_from_poly.py +153 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/diag_to_pix.py +358 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/diag_to_rot.py +449 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/double_flatfield.py +143 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/generate_header.py +261 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/histogram.py +197 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/multicor.py +90 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/nx_z_splitter.py +125 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/parse_reconstruction_log.py +151 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/prepare_weights_double.py +163 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/reconstruct.py +120 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/reconstruct_helical.py +116 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/reduce_dark_flat.py +181 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/rotate.py +162 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/shrink_dataset.py +98 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/stitching.py +85 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/tests/test_reduce_dark_flat.py +78 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/utils.py +33 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/validator.py +110 -0
- 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 +8 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/fft.py +4 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/kernel.py +97 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/medfilt.py +6 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/padding.py +6 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/processing.py +75 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/tests/__init__.py +1 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/utils.py +331 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/__init__.py +12 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/alignment.py +578 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/cor.py +1621 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/cor_sino.py +183 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/distortion.py +112 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/focus.py +362 -0
- 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 +70 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_cor.py +472 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_focus.py +105 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_tilt.py +41 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_translation.py +78 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tilt.py +214 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/translation.py +193 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/utils.py +39 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/__init__.py +2 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/cast_volume.py +371 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/detector_distortion.py +305 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/reader.py +628 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/reader_helical.py +114 -0
- 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 +339 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tests/test_detector_distortion.py +178 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tests/test_writers.py +187 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tiffwriter_zmm.py +99 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/utils.py +263 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/writer.py +892 -0
- 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 +98 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/fftshift.py +6 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/filters.py +24 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/fourier_filters.py +152 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/histogram.py +6 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/histogram_cuda.py +8 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/kernel_base.py +4 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/padding.py +83 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/padding_base.py +6 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/processing_base.py +4 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/rotation.py +6 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/rotation_cuda.py +6 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/tests/__init__.py +1 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/tests/test_binning.py +48 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/tests/test_interpolation.py +70 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/transpose.py +6 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/unsharp.py +4 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/unsharp_cuda.py +6 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/unsharp_opencl.py +8 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/utils.py +117 -0
- 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 +6 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/kernel.py +135 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/memcpy.py +35 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/padding.py +6 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/processing.py +62 -0
- 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 +292 -0
- 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 +265 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/config_validators.py +589 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/datadump.py +164 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/dataset_validator.py +211 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/detector_distortion_provider.py +20 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/estimators.py +1012 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fallback_utils.py +149 -0
- 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 +849 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/chunked_cuda.py +152 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/computations.py +260 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/dataset_validator.py +63 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/nabu_config.py +590 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/processconfig.py +825 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/reconstruction.py +851 -0
- 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 +19 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/fbp.py +147 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/filtering.py +246 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/gridded_accumulator.py +575 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_chunked_regridded.py +1670 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_chunked_regridded_cuda.py +119 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_reconstruction.py +598 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_utils.py +42 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/nabu_config.py +175 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/processconfig.py +62 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/span_strategy.py +483 -0
- 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 +157 -0
- 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 +355 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/test_strategy.py +61 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/utils.py +51 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/weight_balancer.py +101 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/params.py +163 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/processconfig.py +210 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/tests/test_chunk_reader.py +78 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/tests/test_estimators.py +149 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/utils.py +116 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/writer.py +193 -0
- 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 +7 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/alignment.py +11 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ccd.py +161 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ccd_cuda.py +169 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ctf.py +361 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ctf_cuda.py +142 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/distortion.py +92 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/double_flatfield.py +212 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/double_flatfield_cuda.py +174 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/double_flatfield_variable_region.py +68 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/flatfield.py +448 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/flatfield_cuda.py +144 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/flatfield_variable_region.py +79 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/phase.py +425 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/phase_cuda.py +143 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/shift.py +95 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/shift_cuda.py +102 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/tests/__init__.py +1 -0
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- build/lib/nabu/app/tests/test_reduce_dark_flat.py +78 -0
- build/lib/nabu/app/utils.py +33 -0
- build/lib/nabu/app/validator.py +110 -0
- build/lib/nabu/cuda/__init__.py +0 -0
- build/lib/nabu/cuda/convolution.py +8 -0
- build/lib/nabu/cuda/fft.py +4 -0
- build/lib/nabu/cuda/kernel.py +97 -0
- build/lib/nabu/cuda/medfilt.py +6 -0
- build/lib/nabu/cuda/padding.py +6 -0
- build/lib/nabu/cuda/processing.py +75 -0
- build/lib/nabu/cuda/tests/__init__.py +1 -0
- build/lib/nabu/cuda/utils.py +331 -0
- build/lib/nabu/estimation/__init__.py +12 -0
- build/lib/nabu/estimation/alignment.py +578 -0
- build/lib/nabu/estimation/cor.py +1621 -0
- build/lib/nabu/estimation/cor_sino.py +183 -0
- build/lib/nabu/estimation/distortion.py +112 -0
- build/lib/nabu/estimation/focus.py +362 -0
- build/lib/nabu/estimation/tests/__init__.py +0 -0
- build/lib/nabu/estimation/tests/test_alignment.py +70 -0
- build/lib/nabu/estimation/tests/test_cor.py +472 -0
- build/lib/nabu/estimation/tests/test_focus.py +105 -0
- build/lib/nabu/estimation/tests/test_tilt.py +41 -0
- build/lib/nabu/estimation/tests/test_translation.py +78 -0
- build/lib/nabu/estimation/tilt.py +214 -0
- build/lib/nabu/estimation/translation.py +193 -0
- build/lib/nabu/estimation/utils.py +39 -0
- build/lib/nabu/io/__init__.py +2 -0
- build/lib/nabu/io/cast_volume.py +371 -0
- build/lib/nabu/io/detector_distortion.py +305 -0
- build/lib/nabu/io/reader.py +628 -0
- build/lib/nabu/io/reader_helical.py +114 -0
- build/lib/nabu/io/tests/__init__.py +0 -0
- build/lib/nabu/io/tests/test_cast_volume.py +339 -0
- build/lib/nabu/io/tests/test_detector_distortion.py +178 -0
- build/lib/nabu/io/tests/test_writers.py +187 -0
- build/lib/nabu/io/tiffwriter_zmm.py +99 -0
- build/lib/nabu/io/utils.py +263 -0
- build/lib/nabu/io/writer.py +892 -0
- build/lib/nabu/misc/__init__.py +0 -0
- build/lib/nabu/misc/binning.py +98 -0
- build/lib/nabu/misc/fftshift.py +6 -0
- build/lib/nabu/misc/filters.py +24 -0
- build/lib/nabu/misc/fourier_filters.py +152 -0
- build/lib/nabu/misc/histogram.py +6 -0
- build/lib/nabu/misc/histogram_cuda.py +8 -0
- build/lib/nabu/misc/kernel_base.py +4 -0
- build/lib/nabu/misc/padding.py +83 -0
- build/lib/nabu/misc/padding_base.py +6 -0
- build/lib/nabu/misc/processing_base.py +4 -0
- build/lib/nabu/misc/rotation.py +6 -0
- build/lib/nabu/misc/rotation_cuda.py +6 -0
- build/lib/nabu/misc/tests/__init__.py +1 -0
- build/lib/nabu/misc/tests/test_binning.py +48 -0
- build/lib/nabu/misc/tests/test_interpolation.py +70 -0
- build/lib/nabu/misc/transpose.py +6 -0
- build/lib/nabu/misc/unsharp.py +4 -0
- build/lib/nabu/misc/unsharp_cuda.py +6 -0
- build/lib/nabu/misc/unsharp_opencl.py +8 -0
- build/lib/nabu/misc/utils.py +117 -0
- build/lib/nabu/opencl/__init__.py +0 -0
- build/lib/nabu/opencl/fft.py +6 -0
- build/lib/nabu/opencl/kernel.py +135 -0
- build/lib/nabu/opencl/memcpy.py +35 -0
- build/lib/nabu/opencl/padding.py +6 -0
- build/lib/nabu/opencl/processing.py +62 -0
- build/lib/nabu/opencl/tests/__init__.py +0 -0
- build/lib/nabu/opencl/utils.py +292 -0
- build/lib/nabu/pipeline/__init__.py +0 -0
- build/lib/nabu/pipeline/config.py +265 -0
- build/lib/nabu/pipeline/config_validators.py +589 -0
- build/lib/nabu/pipeline/datadump.py +164 -0
- build/lib/nabu/pipeline/dataset_validator.py +211 -0
- build/lib/nabu/pipeline/detector_distortion_provider.py +20 -0
- build/lib/nabu/pipeline/estimators.py +1012 -0
- build/lib/nabu/pipeline/fallback_utils.py +149 -0
- build/lib/nabu/pipeline/fullfield/__init__.py +0 -0
- build/lib/nabu/pipeline/fullfield/chunked.py +849 -0
- build/lib/nabu/pipeline/fullfield/chunked_cuda.py +152 -0
- build/lib/nabu/pipeline/fullfield/computations.py +260 -0
- build/lib/nabu/pipeline/fullfield/dataset_validator.py +63 -0
- build/lib/nabu/pipeline/fullfield/nabu_config.py +590 -0
- build/lib/nabu/pipeline/fullfield/processconfig.py +825 -0
- build/lib/nabu/pipeline/fullfield/reconstruction.py +851 -0
- build/lib/nabu/pipeline/helical/__init__.py +0 -0
- build/lib/nabu/pipeline/helical/dataset_validator.py +19 -0
- build/lib/nabu/pipeline/helical/fbp.py +147 -0
- build/lib/nabu/pipeline/helical/filtering.py +246 -0
- build/lib/nabu/pipeline/helical/gridded_accumulator.py +575 -0
- build/lib/nabu/pipeline/helical/helical_chunked_regridded.py +1670 -0
- build/lib/nabu/pipeline/helical/helical_chunked_regridded_cuda.py +119 -0
- build/lib/nabu/pipeline/helical/helical_reconstruction.py +598 -0
- build/lib/nabu/pipeline/helical/helical_utils.py +42 -0
- build/lib/nabu/pipeline/helical/nabu_config.py +175 -0
- build/lib/nabu/pipeline/helical/processconfig.py +62 -0
- build/lib/nabu/pipeline/helical/span_strategy.py +483 -0
- build/lib/nabu/pipeline/helical/tests/__init__.py +0 -0
- build/lib/nabu/pipeline/helical/tests/test_accumulator.py +157 -0
- build/lib/nabu/pipeline/helical/tests/test_pipeline_elements_full.py +355 -0
- build/lib/nabu/pipeline/helical/tests/test_strategy.py +61 -0
- build/lib/nabu/pipeline/helical/utils.py +51 -0
- build/lib/nabu/pipeline/helical/weight_balancer.py +101 -0
- build/lib/nabu/pipeline/params.py +163 -0
- build/lib/nabu/pipeline/processconfig.py +210 -0
- build/lib/nabu/pipeline/tests/test_chunk_reader.py +78 -0
- build/lib/nabu/pipeline/tests/test_estimators.py +149 -0
- build/lib/nabu/pipeline/utils.py +116 -0
- build/lib/nabu/pipeline/writer.py +193 -0
- build/lib/nabu/pipeline/xrdct/__init__.py +0 -0
- build/lib/nabu/preproc/__init__.py +7 -0
- build/lib/nabu/preproc/alignment.py +11 -0
- build/lib/nabu/preproc/ccd.py +161 -0
- build/lib/nabu/preproc/ccd_cuda.py +169 -0
- build/lib/nabu/preproc/ctf.py +361 -0
- build/lib/nabu/preproc/ctf_cuda.py +142 -0
- build/lib/nabu/preproc/distortion.py +92 -0
- build/lib/nabu/preproc/double_flatfield.py +212 -0
- build/lib/nabu/preproc/double_flatfield_cuda.py +174 -0
- build/lib/nabu/preproc/double_flatfield_variable_region.py +68 -0
- build/lib/nabu/preproc/flatfield.py +448 -0
- build/lib/nabu/preproc/flatfield_cuda.py +144 -0
- build/lib/nabu/preproc/flatfield_variable_region.py +79 -0
- build/lib/nabu/preproc/phase.py +425 -0
- build/lib/nabu/preproc/phase_cuda.py +143 -0
- build/lib/nabu/preproc/shift.py +95 -0
- build/lib/nabu/preproc/shift_cuda.py +102 -0
- build/lib/nabu/preproc/tests/__init__.py +1 -0
- build/lib/nabu/preproc/tests/test_ccd_corr.py +59 -0
- build/lib/nabu/preproc/tests/test_ctf.py +250 -0
- build/lib/nabu/preproc/tests/test_double_flatfield.py +86 -0
- build/lib/nabu/preproc/tests/test_flatfield.py +626 -0
- build/lib/nabu/preproc/tests/test_paganin.py +67 -0
- build/lib/nabu/preproc/tests/test_vshift.py +73 -0
- build/lib/nabu/processing/__init__.py +0 -0
- build/lib/nabu/processing/convolution_cuda.py +375 -0
- build/lib/nabu/processing/fft_base.py +163 -0
- build/lib/nabu/processing/fft_cuda.py +256 -0
- build/lib/nabu/processing/fft_opencl.py +54 -0
- build/lib/nabu/processing/fftshift.py +134 -0
- build/lib/nabu/processing/histogram.py +286 -0
- build/lib/nabu/processing/histogram_cuda.py +103 -0
- build/lib/nabu/processing/kernel_base.py +126 -0
- build/lib/nabu/processing/medfilt_cuda.py +159 -0
- build/lib/nabu/processing/muladd.py +29 -0
- build/lib/nabu/processing/muladd_cuda.py +68 -0
- build/lib/nabu/processing/padding_base.py +71 -0
- build/lib/nabu/processing/padding_cuda.py +75 -0
- build/lib/nabu/processing/padding_opencl.py +77 -0
- build/lib/nabu/processing/processing_base.py +123 -0
- build/lib/nabu/processing/roll_opencl.py +64 -0
- build/lib/nabu/processing/rotation.py +63 -0
- build/lib/nabu/processing/rotation_cuda.py +66 -0
- build/lib/nabu/processing/tests/__init__.py +0 -0
- build/lib/nabu/processing/tests/test_fft.py +268 -0
- build/lib/nabu/processing/tests/test_fftshift.py +71 -0
- build/lib/nabu/processing/tests/test_histogram.py +55 -0
- build/lib/nabu/processing/tests/test_medfilt.py +77 -0
- build/lib/nabu/processing/tests/test_muladd.py +54 -0
- build/lib/nabu/processing/tests/test_padding.py +247 -0
- build/lib/nabu/processing/tests/test_roll.py +63 -0
- build/lib/nabu/processing/tests/test_rotation.py +83 -0
- build/lib/nabu/processing/tests/test_transpose.py +72 -0
- build/lib/nabu/processing/tests/test_unsharp.py +106 -0
- build/lib/nabu/processing/transpose.py +126 -0
- build/lib/nabu/processing/unsharp.py +79 -0
- build/lib/nabu/processing/unsharp_cuda.py +53 -0
- build/lib/nabu/processing/unsharp_opencl.py +75 -0
- build/lib/nabu/reconstruction/__init__.py +3 -0
- build/lib/nabu/reconstruction/cone.py +241 -0
- build/lib/nabu/reconstruction/fbp.py +124 -0
- build/lib/nabu/reconstruction/fbp_base.py +391 -0
- build/lib/nabu/reconstruction/fbp_opencl.py +78 -0
- build/lib/nabu/reconstruction/filtering.py +220 -0
- build/lib/nabu/reconstruction/filtering_cuda.py +103 -0
- build/lib/nabu/reconstruction/filtering_opencl.py +111 -0
- build/lib/nabu/reconstruction/projection.py +240 -0
- build/lib/nabu/reconstruction/reconstructor.py +174 -0
- build/lib/nabu/reconstruction/reconstructor_cuda.py +44 -0
- build/lib/nabu/reconstruction/rings.py +248 -0
- build/lib/nabu/reconstruction/rings_cuda.py +322 -0
- build/lib/nabu/reconstruction/sinogram.py +467 -0
- build/lib/nabu/reconstruction/sinogram_cuda.py +250 -0
- build/lib/nabu/reconstruction/sinogram_opencl.py +40 -0
- build/lib/nabu/reconstruction/tests/__init__.py +1 -0
- build/lib/nabu/reconstruction/tests/test_cone.py +308 -0
- build/lib/nabu/reconstruction/tests/test_deringer.py +220 -0
- build/lib/nabu/reconstruction/tests/test_fbp.py +252 -0
- build/lib/nabu/reconstruction/tests/test_filtering.py +133 -0
- build/lib/nabu/reconstruction/tests/test_halftomo.py +100 -0
- build/lib/nabu/reconstruction/tests/test_projector.py +164 -0
- build/lib/nabu/reconstruction/tests/test_reconstructor.py +93 -0
- build/lib/nabu/reconstruction/tests/test_sino_normalization.py +85 -0
- build/lib/nabu/resources/__init__.py +0 -0
- build/lib/nabu/resources/cli/__init__.py +0 -0
- build/lib/nabu/resources/cor.py +5 -0
- build/lib/nabu/resources/dataset_analyzer.py +469 -0
- build/lib/nabu/resources/gpu.py +169 -0
- build/lib/nabu/resources/logger.py +130 -0
- build/lib/nabu/resources/nxflatfield.py +217 -0
- 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 +104 -0
- build/lib/nabu/resources/tests/test_units.py +47 -0
- build/lib/nabu/resources/utils.py +174 -0
- build/lib/nabu/stitching/__init__.py +0 -0
- build/lib/nabu/stitching/alignment.py +184 -0
- build/lib/nabu/stitching/config.py +1286 -0
- build/lib/nabu/stitching/definitions.py +6 -0
- build/lib/nabu/stitching/frame_composition.py +155 -0
- build/lib/nabu/stitching/overlap.py +373 -0
- build/lib/nabu/stitching/sample_normalization.py +60 -0
- build/lib/nabu/stitching/slurm_utils.py +204 -0
- build/lib/nabu/stitching/tests/__init__.py +0 -0
- build/lib/nabu/stitching/tests/test_alignment.py +99 -0
- build/lib/nabu/stitching/tests/test_config.py +226 -0
- build/lib/nabu/stitching/tests/test_frame_composition.py +180 -0
- build/lib/nabu/stitching/tests/test_overlap.py +98 -0
- build/lib/nabu/stitching/tests/test_sample_normalization.py +49 -0
- build/lib/nabu/stitching/tests/test_slurm_utils.py +146 -0
- build/lib/nabu/stitching/tests/test_utils.py +21 -0
- build/lib/nabu/stitching/tests/test_z_stitching.py +1183 -0
- build/lib/nabu/stitching/utils.py +563 -0
- build/lib/nabu/stitching/z_stitching.py +2279 -0
- build/lib/nabu/tests.py +51 -0
- build/lib/nabu/testutils.py +375 -0
- build/lib/nabu/thirdparty/__init__.py +0 -0
- build/lib/nabu/thirdparty/algotom_convert_sino.py +276 -0
- build/lib/nabu/thirdparty/pore3d_deringer_munch.py +108 -0
- build/lib/nabu/thirdparty/tomocupy_remove_stripe.py +586 -0
- build/lib/nabu/thirdparty/tomopy_phase.py +239 -0
- build/lib/nabu/thirdparty/tomwer_load_flats_darks.py +162 -0
- build/lib/nabu/utils.py +836 -0
- nabu/__init__.py +1 -1
- nabu/estimation/cor.py +2 -2
- nabu/io/cast_volume.py +10 -2
- nabu/pipeline/estimators.py +13 -7
- nabu/resources/dataset_analyzer.py +15 -6
- nabu/stitching/config.py +2 -2
- nabu/stitching/z_stitching.py +3 -1
- {nabu-2024.1.0rc3.dist-info → nabu-2024.1.1.dist-info}/METADATA +1 -1
- nabu-2024.1.1.dist-info/RECORD +2375 -0
- nabu-2024.1.1.dist-info/top_level.txt +4 -0
- doc/doc_config.py +0 -32
- nabu-2024.1.0rc3.dist-info/RECORD +0 -296
- nabu-2024.1.0rc3.dist-info/top_level.txt +0 -2
- {nabu-2024.1.0rc3.dist-info → nabu-2024.1.1.dist-info}/LICENSE +0 -0
- {nabu-2024.1.0rc3.dist-info → nabu-2024.1.1.dist-info}/WHEEL +0 -0
- {nabu-2024.1.0rc3.dist-info → nabu-2024.1.1.dist-info}/entry_points.txt +0 -0
build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/fbp.py
ADDED
@@ -0,0 +1,124 @@
|
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1
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+
import numpy as np
|
2
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+
import pycuda.driver as cuda
|
3
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from ..utils import updiv, get_cuda_srcfile
|
4
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+
from ..cuda.utils import copy_array, check_textures_availability
|
5
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+
from ..cuda.processing import CudaProcessing
|
6
|
+
from ..cuda.kernel import CudaKernel
|
7
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+
from .filtering_cuda import CudaSinoFilter
|
8
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+
from .sinogram_cuda import CudaSinoMult
|
9
|
+
from .fbp_base import BackprojectorBase
|
10
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+
|
11
|
+
|
12
|
+
class CudaBackprojector(BackprojectorBase):
|
13
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+
backend = "cuda"
|
14
|
+
kernel_filename = "backproj.cu"
|
15
|
+
backend_processing_class = CudaProcessing
|
16
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+
SinoFilterClass = CudaSinoFilter
|
17
|
+
SinoMultClass = CudaSinoMult
|
18
|
+
|
19
|
+
def _check_textures_availability(self):
|
20
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+
self._use_textures = self.extra_options.get("use_textures", True) and check_textures_availability()
|
21
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+
|
22
|
+
def _get_kernel_signature(self):
|
23
|
+
kern_full_sig = list("PPiifiiffPPPf")
|
24
|
+
if self._axis_correction is None:
|
25
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+
kern_full_sig[11] = ""
|
26
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+
if self._use_textures:
|
27
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+
# texture references - no object is passed (deprecated, removed in Cuda 12)
|
28
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+
kern_full_sig[1] = ""
|
29
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+
return "".join(kern_full_sig)
|
30
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+
|
31
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+
def _get_kernel_options(self):
|
32
|
+
super()._get_kernel_options()
|
33
|
+
self._kernel_options.update(
|
34
|
+
{
|
35
|
+
"file_name": get_cuda_srcfile(self.kernel_filename),
|
36
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+
"kernel_signature": self._get_kernel_signature(),
|
37
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+
"texture_name": "tex_projections",
|
38
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+
}
|
39
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+
)
|
40
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+
|
41
|
+
def _prepare_kernel_args(self):
|
42
|
+
super()._prepare_kernel_args()
|
43
|
+
self.kern_proj_kwargs.update(
|
44
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+
{
|
45
|
+
"shared_size": self._kernel_options["shared_size"],
|
46
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+
}
|
47
|
+
)
|
48
|
+
# texture references - no object is passed (deprecated, removed in Cuda 12)
|
49
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+
if self._use_textures:
|
50
|
+
self.kern_proj_args.pop(1)
|
51
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+
else:
|
52
|
+
self._d_sino = self._processing.allocate_array("_d_sino", self.sino_shape)
|
53
|
+
self.kern_proj_args[1] = self._d_sino.gpudata
|
54
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+
|
55
|
+
def _prepare_textures(self):
|
56
|
+
if self._use_textures:
|
57
|
+
self.texref_proj = self.gpu_projector.module.get_texref(self._kernel_options["texture_name"])
|
58
|
+
self.texref_proj.set_filter_mode(cuda.filter_mode.LINEAR)
|
59
|
+
self.gpu_projector.prepare(self._kernel_options["kernel_signature"], [self.texref_proj])
|
60
|
+
# Bind texture
|
61
|
+
self._d_sino_cua = cuda.np_to_array(np.zeros(self.sino_shape, "f"), "C")
|
62
|
+
self.texref_proj.set_array(self._d_sino_cua)
|
63
|
+
else:
|
64
|
+
# d_sino_ref = self._d_sino.gpudata
|
65
|
+
# self.kern_proj_args.insert(2, d_sino_ref)
|
66
|
+
self.gpu_projector.prepare(self._kernel_options["kernel_signature"], [])
|
67
|
+
|
68
|
+
def _compile_kernels(self):
|
69
|
+
self._prepare_kernel_args()
|
70
|
+
if self._use_textures:
|
71
|
+
self._kernel_options["sourcemodule_options"].append("-DUSE_TEXTURES")
|
72
|
+
self.gpu_projector = CudaKernel(
|
73
|
+
self._kernel_options["kernel_name"],
|
74
|
+
filename=self._kernel_options["file_name"],
|
75
|
+
options=self._kernel_options["sourcemodule_options"],
|
76
|
+
)
|
77
|
+
if self.halftomo and self.rot_center < self.dwidth:
|
78
|
+
self.sino_mult = CudaSinoMult(self.sino_shape, self.rot_center, ctx=self._processing.ctx)
|
79
|
+
self._prepare_textures() # has to be done after compilation for Cuda (to bind texture to built kernel)
|
80
|
+
|
81
|
+
def _transfer_to_texture(self, sino, do_checks=True):
|
82
|
+
if self._use_textures:
|
83
|
+
copy_array(self._d_sino_cua, sino, check=do_checks)
|
84
|
+
else:
|
85
|
+
if id(self._d_sino) == id(sino):
|
86
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+
return
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self._d_sino[:] = sino[:]
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# COMPAT.
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Backprojector = CudaBackprojector
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class PolarBackprojector(Backprojector):
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"""
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Cuda Backprojector with output in polar coordinates.
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"""
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cuda_fname = "backproj_polar.cu"
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cuda_kernel_name = "backproj_polar"
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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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self.slice_shape = (self.n_angles, self.n_x)
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# patch parent method:
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def _set_slice_roi(self, slice_roi):
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if slice_roi is not None:
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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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+
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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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+
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# patch parent method: update kernel args
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def _compile_kernels(self):
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n_y = self.n_y
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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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@@ -0,0 +1,391 @@
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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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"""
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Base class for backprojectors.
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"""
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backend = "numpy"
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default_padding_mode = "zeros"
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kernel_name = "backproj"
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default_extra_options = {
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"padding_mode": None,
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"axis_correction": None,
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"centered_axis": False,
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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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backend_processing_class = ProcessingBase
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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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+
|
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|
+
Parameters
|
50
|
+
-----------
|
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+
sino_shape: tuple
|
52
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+
Shape of the sinogram, in the form `(n_angles, detector_width)`
|
53
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+
(for backprojecting one sinogram) or `(n_sinos, n_angles, detector_width)`.
|
54
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+
slice_shape: int or tuple, optional
|
55
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+
Shape of the slice. By default, the slice shape is (n_x, n_x) where
|
56
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+
`n_x = detector_width`
|
57
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+
angles: array-like, optional
|
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+
Rotation anles in radians.
|
59
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+
By default, angles are equispaced between [0, pi[.
|
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+
rot_center: float, optional
|
61
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+
Rotation axis position. Default is `(detector_width - 1)/2.0`
|
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+
padding_mode: str, optional
|
63
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+
Padding mode when filtering the sinogram. Can be "zeros" (default) or "edges".
|
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+
filter_name: str, optional
|
65
|
+
Name of the filter for filtered-backprojection.
|
66
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+
slice_roi: tuple, optional.
|
67
|
+
Whether to backproject in a restricted area.
|
68
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+
If set, it must be in the form (start_x, end_x, start_y, end_y).
|
69
|
+
`end_x` and `end_y` are non inclusive ! For example if the detector has
|
70
|
+
2048 pixels horizontally, then you can choose `start_x=0` and `end_x=2048`.
|
71
|
+
If one of the value is set to None, it is replaced with a default value
|
72
|
+
(0 for start, n_x and n_y for end)
|
73
|
+
scale_factor: float, optional
|
74
|
+
Scaling factor for backprojection.
|
75
|
+
For example, to get the linear absorption coefficient in 1/cm,
|
76
|
+
this factor has to be set as the pixel size in cm.
|
77
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+
DEPRECATED - please use this parameter in "extra_options"
|
78
|
+
extra_options: dict, optional
|
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+
Advanced extra options.
|
80
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+
See the "Extra options" section for more information.
|
81
|
+
backend_options: dict, optional
|
82
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+
OpenCL/Cuda options passed to the OpenCLProcessing or CudaProcessing class.
|
83
|
+
|
84
|
+
Other parameters
|
85
|
+
-----------------
|
86
|
+
extra_options: dict, optional
|
87
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+
Dictionary with a set of advanced options. The default are the following:
|
88
|
+
- "padding_mode": "zeros"
|
89
|
+
Padding mode when filtering the sinogram. Can be "zeros" or "edges".
|
90
|
+
DEPRECATED - please use "padding_mode" directly in parameters.
|
91
|
+
- "axis_correction": None
|
92
|
+
Whether to set a correction for the rotation axis.
|
93
|
+
If set, this should be an array with as many elements as the number
|
94
|
+
of angles. This is useful when there is an horizontal displacement
|
95
|
+
of the rotation axis.
|
96
|
+
- centered_axis: bool
|
97
|
+
Whether to "center" the slice on the rotation axis position.
|
98
|
+
If set to True, then the reconstructed region is centered on the rotation axis.
|
99
|
+
- scale_factor: float
|
100
|
+
Scaling factor for backprojection.
|
101
|
+
For example, to get the linear absorption coefficient in 1/cm,
|
102
|
+
this factor has to be set as the pixel size in cm.
|
103
|
+
- clip_outer_circle: False
|
104
|
+
Whether to set to zero the pixels outside the reconstruction mask
|
105
|
+
- filter_cutoff: float
|
106
|
+
Cut-off frequency usef for Fourier filter. Default is 1.0
|
107
|
+
"""
|
108
|
+
self._processing = self.backend_processing_class(**(backend_options or {}))
|
109
|
+
self._configure_extra_options(scale_factor, padding_mode, extra_options=extra_options)
|
110
|
+
self._check_textures_availability()
|
111
|
+
self._init_geometry(sino_shape, slice_shape, angles, rot_center, halftomo, slice_roi)
|
112
|
+
self._init_filter(filter_name)
|
113
|
+
self._allocate_memory()
|
114
|
+
self._compute_angles()
|
115
|
+
self._compile_kernels()
|
116
|
+
|
117
|
+
def _configure_extra_options(self, scale_factor, padding_mode, extra_options=None):
|
118
|
+
extra_options = extra_options or {}
|
119
|
+
# compat.
|
120
|
+
scale_factor = None
|
121
|
+
if scale_factor is not None:
|
122
|
+
deprecation_warning(
|
123
|
+
"Please use the parameter 'scale_factor' in the 'extra_options' dict",
|
124
|
+
do_print=True,
|
125
|
+
func_name="fbp_scale_factor",
|
126
|
+
)
|
127
|
+
scale_factor = extra_options.get("scale_factor", None) or scale_factor or 1.0
|
128
|
+
#
|
129
|
+
if "padding_mode" in extra_options:
|
130
|
+
deprecation_warning(
|
131
|
+
"Please use 'padding_mode' directly in Backprojector arguments, not in 'extra_options'",
|
132
|
+
do_print=True,
|
133
|
+
func_name="fbp_padding_mode",
|
134
|
+
)
|
135
|
+
#
|
136
|
+
self._backproj_scale_factor = scale_factor
|
137
|
+
self._axis_array = None
|
138
|
+
self.extra_options = self.default_extra_options.copy()
|
139
|
+
self.extra_options.update(extra_options)
|
140
|
+
self.padding_mode = padding_mode or self.extra_options["padding_mode"] or self.default_padding_mode
|
141
|
+
self._axis_array = self.extra_options["axis_correction"]
|
142
|
+
|
143
|
+
def _init_geometry(self, sino_shape, slice_shape, angles, rot_center, halftomo, slice_roi):
|
144
|
+
if slice_shape is not None and slice_roi is not None:
|
145
|
+
raise ValueError("slice_shape and slice_roi cannot be used together")
|
146
|
+
self.sino_shape = sino_shape
|
147
|
+
if len(sino_shape) == 2:
|
148
|
+
n_angles, dwidth = sino_shape
|
149
|
+
else:
|
150
|
+
raise ValueError("Expected 2D sinogram")
|
151
|
+
self.dwidth = dwidth
|
152
|
+
self.halftomo = halftomo
|
153
|
+
if rot_center is None:
|
154
|
+
if halftomo:
|
155
|
+
raise ValueError("Need to know 'rot_center' when using halftomo")
|
156
|
+
rot_center = (self.dwidth - 1) / 2.0
|
157
|
+
self.rot_center = rot_center
|
158
|
+
self._set_slice_shape(slice_shape)
|
159
|
+
self.axis_pos = self.rot_center
|
160
|
+
self._set_angles(angles, n_angles)
|
161
|
+
self._set_slice_roi(slice_roi)
|
162
|
+
#
|
163
|
+
# offset = start - move
|
164
|
+
# move = 0 if not(centered_axis) else start + (n-1)/2. - c
|
165
|
+
if self.extra_options["centered_axis"]:
|
166
|
+
self.offsets = {
|
167
|
+
"x": self.rot_center - (self.n_x - 1) / 2.0,
|
168
|
+
"y": self.rot_center - (self.n_y - 1) / 2.0,
|
169
|
+
}
|
170
|
+
#
|
171
|
+
self._set_axis_corr()
|
172
|
+
|
173
|
+
def _set_slice_shape(self, slice_shape):
|
174
|
+
if not (self.halftomo):
|
175
|
+
n_x = n_y = self.dwidth
|
176
|
+
else:
|
177
|
+
n_x = n_y = get_extended_sinogram_width(self.dwidth, self.rot_center)
|
178
|
+
if slice_shape is not None:
|
179
|
+
if np.isscalar(slice_shape):
|
180
|
+
slice_shape = (slice_shape, slice_shape)
|
181
|
+
n_y, n_x = slice_shape
|
182
|
+
self.n_x = n_x
|
183
|
+
self.n_y = n_y
|
184
|
+
self.slice_shape = (n_y, n_x)
|
185
|
+
|
186
|
+
def _set_angles(self, angles, n_angles):
|
187
|
+
self.n_angles = n_angles
|
188
|
+
if angles is None:
|
189
|
+
angles = n_angles
|
190
|
+
if np.isscalar(angles):
|
191
|
+
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
|
+
assert len(angles) == self.n_angles, "expected %d angles but got %d" % (len(angles), self.n_angles)
|
196
|
+
self.angles = angles
|
197
|
+
|
198
|
+
def _set_slice_roi(self, slice_roi):
|
199
|
+
self.offsets = {"x": 0, "y": 0}
|
200
|
+
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
|
+
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
|
+
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))
|
295
|
+
grid = (updiv(updiv(self.n_x, block[0]), 2), updiv(updiv(self.n_y, block[1]), 2))
|
296
|
+
if self.extra_options["clip_outer_circle"]:
|
297
|
+
sourcemodule_options.append("-DCLIP_OUTER_CIRCLE")
|
298
|
+
shared_size = int(np.prod(block)) * 2
|
299
|
+
if self._axis_correction is not None:
|
300
|
+
sourcemodule_options.append("-DDO_AXIS_CORRECTION")
|
301
|
+
shared_size += int(np.prod(block))
|
302
|
+
shared_size *= 4 # sizeof(float32)
|
303
|
+
self._kernel_options = {
|
304
|
+
"kernel_name": self.kernel_name,
|
305
|
+
"sourcemodule_options": sourcemodule_options,
|
306
|
+
"grid": grid,
|
307
|
+
"block": block,
|
308
|
+
"shared_size": shared_size,
|
309
|
+
}
|
310
|
+
|
311
|
+
def _prepare_kernel_args(self):
|
312
|
+
self._get_kernel_options()
|
313
|
+
self.kern_proj_args = [
|
314
|
+
None, # output d_slice holder
|
315
|
+
None, # placeholder for sino (OpenCL or Cuda+no-texture)
|
316
|
+
np.int32(self.n_angles),
|
317
|
+
np.int32(self.dwidth),
|
318
|
+
np.float32(self.axis_pos),
|
319
|
+
np.int32(self.n_x),
|
320
|
+
np.int32(self.n_y),
|
321
|
+
np.float32(self.offsets["x"]),
|
322
|
+
np.float32(self.offsets["y"]),
|
323
|
+
self._d_cos,
|
324
|
+
self._d_msin,
|
325
|
+
np.float32(self._backproj_scale_factor),
|
326
|
+
]
|
327
|
+
if self._axis_correction is not None:
|
328
|
+
self.kern_proj_args.insert(-1, self._d_axcorr)
|
329
|
+
self.kern_proj_kwargs = {
|
330
|
+
"grid": self._kernel_options["grid"],
|
331
|
+
"block": self._kernel_options["block"],
|
332
|
+
}
|
333
|
+
|
334
|
+
def _set_output(self, output, check=False):
|
335
|
+
self._output_is_ndarray = isinstance(output, np.ndarray)
|
336
|
+
if output is None or self._output_is_ndarray:
|
337
|
+
self._processing.allocate_array("_d_slice", self.slice_shape, dtype=np.float32)
|
338
|
+
return self._processing._d_slice # pylint: disable=E1101
|
339
|
+
if check:
|
340
|
+
assert output.dtype == np.float32
|
341
|
+
assert output.shape == self.slice_shape, "Expected output shape %s but got %s" % (
|
342
|
+
self.slice_shape,
|
343
|
+
output.shape,
|
344
|
+
)
|
345
|
+
return output
|
346
|
+
|
347
|
+
def _set_kernel_slice_arg(self, d_slice):
|
348
|
+
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
|
@@ -0,0 +1,78 @@
|
|
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
|