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/processing/unsharp_opencl.py +0 -75
- build/lib/nabu/reconstruction/__init__.py +0 -3
- build/lib/nabu/reconstruction/cone.py +0 -241
- build/lib/nabu/reconstruction/fbp.py +0 -124
- build/lib/nabu/reconstruction/fbp_base.py +0 -391
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- build/lib/nabu/reconstruction/filtering_opencl.py +0 -111
- build/lib/nabu/reconstruction/projection.py +0 -240
- build/lib/nabu/reconstruction/reconstructor.py +0 -174
- build/lib/nabu/reconstruction/reconstructor_cuda.py +0 -44
- build/lib/nabu/reconstruction/rings.py +0 -248
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- build/lib/nabu/reconstruction/sinogram.py +0 -467
- build/lib/nabu/reconstruction/sinogram_cuda.py +0 -250
- build/lib/nabu/reconstruction/sinogram_opencl.py +0 -40
- build/lib/nabu/reconstruction/tests/__init__.py +0 -1
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- build/lib/nabu/reconstruction/tests/test_filtering.py +0 -133
- build/lib/nabu/reconstruction/tests/test_halftomo.py +0 -100
- build/lib/nabu/reconstruction/tests/test_projector.py +0 -164
- build/lib/nabu/reconstruction/tests/test_reconstructor.py +0 -93
- build/lib/nabu/reconstruction/tests/test_sino_normalization.py +0 -85
- build/lib/nabu/resources/__init__.py +0 -0
- build/lib/nabu/resources/cli/__init__.py +0 -0
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- build/lib/nabu/resources/dataset_analyzer.py +0 -469
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- build/lib/nabu/resources/logger.py +0 -130
- build/lib/nabu/resources/nxflatfield.py +0 -217
- build/lib/nabu/resources/templates/__init__.py +0 -0
- build/lib/nabu/resources/tests/__init__.py +0 -0
- build/lib/nabu/resources/tests/test_nxflatfield.py +0 -104
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- build/lib/nabu/stitching/alignment.py +0 -184
- build/lib/nabu/stitching/config.py +0 -1286
- build/lib/nabu/stitching/definitions.py +0 -6
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- build/lib/nabu/stitching/overlap.py +0 -373
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- build/lib/nabu/stitching/tests/__init__.py +0 -0
- build/lib/nabu/stitching/tests/test_alignment.py +0 -99
- build/lib/nabu/stitching/tests/test_config.py +0 -226
- build/lib/nabu/stitching/tests/test_frame_composition.py +0 -180
- build/lib/nabu/stitching/tests/test_overlap.py +0 -98
- build/lib/nabu/stitching/tests/test_sample_normalization.py +0 -49
- build/lib/nabu/stitching/tests/test_slurm_utils.py +0 -146
- build/lib/nabu/stitching/tests/test_utils.py +0 -21
- build/lib/nabu/stitching/tests/test_z_stitching.py +0 -1183
- build/lib/nabu/stitching/utils.py +0 -563
- build/lib/nabu/stitching/z_stitching.py +0 -2279
- build/lib/nabu/tests.py +0 -51
- build/lib/nabu/testutils.py +0 -375
- build/lib/nabu/thirdparty/__init__.py +0 -0
- build/lib/nabu/thirdparty/algotom_convert_sino.py +0 -276
- build/lib/nabu/thirdparty/pore3d_deringer_munch.py +0 -108
- build/lib/nabu/thirdparty/tomocupy_remove_stripe.py +0 -586
- build/lib/nabu/thirdparty/tomopy_phase.py +0 -239
- build/lib/nabu/thirdparty/tomwer_load_flats_darks.py +0 -162
- build/lib/nabu/utils.py +0 -836
- nabu-2024.1.1.dist-info/RECORD +0 -2375
- nabu-2024.1.1.dist-info/top_level.txt +0 -4
- {build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app → nabu/app/tests}/__init__.py +0 -0
- {nabu-2024.1.1.dist-info → nabu-2024.1.2.dist-info}/LICENSE +0 -0
- {nabu-2024.1.1.dist-info → nabu-2024.1.2.dist-info}/entry_points.txt +0 -0
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from ...preproc.flatfield import FlatFieldArrays
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import numpy as np
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class GriddedAccumulator:
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def __init__(
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gridded_radios,
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gridded_weights,
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diagnostic_radios,
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diagnostic_weights,
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diagnostic_angles,
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diagnostic_zpix_transl,
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dark=None,
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flats=None,
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weights=None,
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"""
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This class creates, for a selected volume slab, a standard set of radios from an helical dataset.
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Parameters
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==========
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gridded_radios : 3D np.array
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this is the stack of new radios which will be resynthetised, by this class,
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for a selected slab.
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The object is initialised with this array, and this array will accumulate, during subsequent
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calls to method extract_preprocess_with_flats, the sum of the transformed contributions
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obtained from the arguments of the mentioned method (extract_preprocess_with_flats).
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gridded_weights : 3d np.array
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same shape as gridded_radios, but it will accumulate the weights, during calls to
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extract_preprocess_with_flats
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diag_zpro_run: int
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if > 0 then only the diagnostics are filled, and no accumulation is done
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diagnostic_searched_angles_rad_clipped:
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the angles between 0 and 2pi. The contributions to diagnostic will be searched for these angles
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plus for the same angles + 2pi ( following turn)
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diagnostic_radios : 3d np.array, a stack composed of
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each radio must have the same size as a radio of the gridded_radios argument.
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During the calls to extract_preprocess_with_flats methods,
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the radios will collect the transformed data for the angles given by diagnostic_searched_angles_rad_clipped and redundancy
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diagnostic_weights: 3d np.array a stack composed of two radios
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where no data is available, or where the weight is null)
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diagnostic_angles : 1D np.array
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to diagnostic_radios have been summed.
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diagnostic_zpix_transl: 1D np.array
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same as for diagnostic_angles, but for vertical translation in pixels
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dark: None or 2D np.array
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radios_srcurrent: 1D np.array
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the machine current for every radio
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the machine current for every flat
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the projection index corresponding to the flats
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the stack of flats. Each flat must have the shape of the detector (generally larger that a radio of gridded_radios)
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The flats, if given, are subtracted of the dark, if given, and the result is used to normalise the data.
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weights : None or 2D np.array
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If not given each data pixel will be considered with unit weight.
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double_flat = None or 2D np.array
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"""
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self.diag_zpro_run = diag_zpro_run
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self.gridded_weights = gridded_weights
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self.diagnostic_radios = diagnostic_radios
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self.diagnostic_weights = diagnostic_weights
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self.diagnostic_zpix_transl = diagnostic_zpix_transl
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self.diagnostic_searched_angles_rad_clipped = diagnostic_searched_angles_rad_clipped
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|
-
self.dark = dark
|
94
|
-
|
95
|
-
self.radios_srcurrent = radios_srcurrent
|
96
|
-
|
97
|
-
self.flats_srcurrent = flats_srcurrent
|
98
|
-
|
99
|
-
self.flat_indexes = flat_indexes
|
100
|
-
self.flat_indexes_reverse_map = dict(
|
101
|
-
[(global_index, local_index) for (local_index, global_index) in enumerate(flat_indexes)]
|
102
|
-
)
|
103
|
-
self.flats = flats
|
104
|
-
self.weights = weights
|
105
|
-
self.double_flat = double_flat
|
106
|
-
|
107
|
-
def extract_preprocess_with_flats(
|
108
|
-
self,
|
109
|
-
subchunk_slice,
|
110
|
-
subchunk_file_indexes,
|
111
|
-
chunk_info,
|
112
|
-
subr_start_end,
|
113
|
-
dtasrc_start_end,
|
114
|
-
data_raw,
|
115
|
-
radios_angular_range_slicing,
|
116
|
-
):
|
117
|
-
"""
|
118
|
-
This functions is meant to be called providing, each time, a subset of the data
|
119
|
-
which are needed to reconstruct a chunk (to reconstruct a slab).
|
120
|
-
When all the necessary data have flown through the subsequent calls to this method,
|
121
|
-
the accumulators are ready.
|
122
|
-
|
123
|
-
Parameters
|
124
|
-
==========
|
125
|
-
subchunk_slice: an object of the python class "slice"
|
126
|
-
this slice slices the angular domain which corresponds to the useful
|
127
|
-
projections which are useful for the chunk, and whose informations
|
128
|
-
are contained in the companion argument "chunk_info"
|
129
|
-
Such slicing correspond to the angular subset, for which we are providing
|
130
|
-
data_raw
|
131
|
-
subchunk_file_indexes: a sequence of integers.
|
132
|
-
they correspond to the projection numbers from which the data in data_raw are coming.
|
133
|
-
They are used to interpolate between falt fields
|
134
|
-
chunk_info: an object returned by the get_chunk_info of the SpanStrategy class
|
135
|
-
this object must have the following members, which relates to the wanted chunk
|
136
|
-
|
137
|
-
angle_index_span: a pair of integers indicating the start and the end of useful angles
|
138
|
-
in the array of all the scan angle self.projection_angles_deg
|
139
|
-
span_v: a pair of two integers indicating the start and end of the span relatively to the lowest value
|
140
|
-
of array self.total_view_heights
|
141
|
-
integer_shift_v: an array, containing for each one of the useful projections of the span,
|
142
|
-
the integer part of vertical shift to be used in cropping,
|
143
|
-
fract_complement_to_integer_shift_v :
|
144
|
-
the fractional remainder for cropping.
|
145
|
-
z_pix_per_proj: an array, containing for each to be used projection of the span
|
146
|
-
the vertical shift
|
147
|
-
x_pix_per_proj: ....the horizontal shift
|
148
|
-
angles_rad : an array, for each useful projection of the chunk the angle in radian
|
149
|
-
subr_start_end: a pair of integers
|
150
|
-
the start height, and the end height, of the slab for which we are collecting the data.
|
151
|
-
The number are given with the same logic as for member span_v of the chunk_info.
|
152
|
-
Without the phase margin, when the phase margin is zero, hey would correspond exactly to
|
153
|
-
the start and end, vertically, of the reconstructed slices.
|
154
|
-
dtasrc_start_end: a pair of integers
|
155
|
-
This number are relative to the detector ( they are detector line indexes).
|
156
|
-
They indicated, vertically, the detector portion the data_raw data correspond to
|
157
|
-
data_raw: np.array 3D
|
158
|
-
the data which correspond to a limited detector stripe and a limited angular subset
|
159
|
-
radios_angular_range_slicing:
|
160
|
-
my_subsampled_indexes is important in order to compare the
|
161
|
-
radios positions with respect to the flat position, and these position
|
162
|
-
are given as the sequential acquisition number which counts everything ( flats, darks, radios )
|
163
|
-
Insteqd, in order to access array which spans only the radios, we need to have an idea of where we are.
|
164
|
-
this is provided by radios_angular_range_slicing which addresses the radios domain
|
165
|
-
|
166
|
-
"""
|
167
|
-
|
168
|
-
# the object below is going to containing some auxiliary variable that are use to reframe the data.
|
169
|
-
# This object is used to pass in a compact way such informations to different methods.
|
170
|
-
# The informations are extracted from chunk info
|
171
|
-
reframing_infos = self._ReframingInfos(
|
172
|
-
chunk_info, subchunk_slice, subr_start_end, dtasrc_start_end, subchunk_file_indexes
|
173
|
-
)
|
174
|
-
|
175
|
-
# give the proper dimensioning to an auxiliary stack which will contain the reframed data extracted
|
176
|
-
# from the treatement of the sub-chunk
|
177
|
-
radios_subset = np.zeros(
|
178
|
-
[data_raw.shape[0], subr_start_end[1] - subr_start_end[0], data_raw.shape[2]], np.float32
|
179
|
-
)
|
180
|
-
|
181
|
-
# ... and in the same way we dimension the container for the associated reframed weights.
|
182
|
-
radios_weights_subset = np.zeros(
|
183
|
-
[data_raw.shape[0], subr_start_end[1] - subr_start_end[0], data_raw.shape[2]], np.float32
|
184
|
-
)
|
185
|
-
|
186
|
-
# extraction of the data
|
187
|
-
self._extract_preprocess_with_flats(
|
188
|
-
data_raw, reframing_infos, chunk_info, radios_subset, radios_angular_range_slicing
|
189
|
-
)
|
190
|
-
|
191
|
-
if self.weights is not None:
|
192
|
-
# ... and, if required, extraction of the associated weights
|
193
|
-
wdata_read = self.weights.data[reframing_infos.dtasrc_start_z : reframing_infos.dtasrc_end_z]
|
194
|
-
self._extract_preprocess_with_flats(
|
195
|
-
wdata_read, reframing_infos, chunk_info, radios_weights_subset, it_is_weight=True
|
196
|
-
)
|
197
|
-
|
198
|
-
else:
|
199
|
-
radios_weights_subset[:] = 1.0
|
200
|
-
|
201
|
-
# and the remaining part is a simple projection over the accumulators, for
|
202
|
-
# the data and for the weights
|
203
|
-
my_angles = chunk_info.angles_rad[subchunk_slice]
|
204
|
-
|
205
|
-
n_gridded_angles = self.gridded_radios.shape[0]
|
206
|
-
|
207
|
-
my_i_float = my_angles * (n_gridded_angles / (2 * math.pi))
|
208
|
-
|
209
|
-
tmp_i_rounded = np.floor(my_i_float).astype(np.int32)
|
210
|
-
my_epsilon = my_i_float - tmp_i_rounded
|
211
|
-
my_i0 = np.mod(tmp_i_rounded, n_gridded_angles)
|
212
|
-
my_i1 = np.mod(my_i0 + 1, n_gridded_angles)
|
213
|
-
|
214
|
-
if self.diag_zpro_run:
|
215
|
-
# these are used only when collection the diagnostics
|
216
|
-
|
217
|
-
# an estimation of the angular step
|
218
|
-
my_angle_step_rad = abs(np.diff(chunk_info.angles_rad[subchunk_slice]).mean())
|
219
|
-
my_angles_02pi = np.mod(my_angles, 2 * np.pi)
|
220
|
-
# bins are delimited by ticks
|
221
|
-
ticks = np.empty(2 * len(self.diagnostic_searched_angles_rad_clipped), "f")
|
222
|
-
ticks[::2] = self.diagnostic_searched_angles_rad_clipped - my_angle_step_rad / 2
|
223
|
-
ticks[1::2] = ticks[::2] + my_angle_step_rad
|
224
|
-
|
225
|
-
for i0, epsilon, i1, data, weight, original_angle, original_zpix_transl in zip(
|
226
|
-
my_i0,
|
227
|
-
my_epsilon,
|
228
|
-
my_i1,
|
229
|
-
radios_subset,
|
230
|
-
radios_weights_subset,
|
231
|
-
chunk_info.angles_rad[subchunk_slice],
|
232
|
-
chunk_info.z_pix_per_proj[subchunk_slice],
|
233
|
-
):
|
234
|
-
data_token = data * weight
|
235
|
-
|
236
|
-
if not self.diag_zpro_run:
|
237
|
-
self.gridded_radios[i0] += data_token * (1 - epsilon)
|
238
|
-
self.gridded_radios[i1] += data_token * epsilon
|
239
|
-
|
240
|
-
self.gridded_weights[i0] += weight * (1 - epsilon)
|
241
|
-
self.gridded_weights[i1] += weight * epsilon
|
242
|
-
|
243
|
-
# building the intervals around the diagnostic angles
|
244
|
-
|
245
|
-
if self.diag_zpro_run:
|
246
|
-
my_i0 = np.searchsorted(ticks, my_angles_02pi)
|
247
|
-
|
248
|
-
for i0, a02pi, data, weight, original_angle, original_zpix_transl in zip(
|
249
|
-
my_i0,
|
250
|
-
my_angles_02pi,
|
251
|
-
radios_subset,
|
252
|
-
radios_weights_subset,
|
253
|
-
chunk_info.angles_rad[subchunk_slice],
|
254
|
-
chunk_info.z_pix_per_proj[subchunk_slice],
|
255
|
-
):
|
256
|
-
if i0 % 2 == 0:
|
257
|
-
# not in an intervals
|
258
|
-
continue
|
259
|
-
|
260
|
-
# There is a contribution to the first regridded radio ( the one indexed by 0)
|
261
|
-
# We build two diagnostics for the contributions to this radio.
|
262
|
-
# The first for the first pass (i_diag=0)
|
263
|
-
# The second for the second pass if any (i_diag=1)
|
264
|
-
|
265
|
-
# To discriminate we introduce
|
266
|
-
# An angular margin beyond which we know that a possible contribution
|
267
|
-
# is coming from another turn
|
268
|
-
|
269
|
-
safe_angular_margin = 3.14 / 40
|
270
|
-
|
271
|
-
my_dist = abs(
|
272
|
-
a02pi - self.diagnostic_searched_angles_rad_clipped[(i0 - 1) // 2 : (i0 - 1) // 2 + 1].mean()
|
273
|
-
)
|
274
|
-
|
275
|
-
# print(" i0 ", i0, " original_angle ", original_angle, " a02pi" , a02pi, " my_dist " , my_dist)
|
276
|
-
|
277
|
-
# consider fist pass and second possible pass. There might be further passes which we dont consider here
|
278
|
-
i_diag_list = [(i0 - 1) // 2, (i0 - 1) // 2 + len(self.diagnostic_searched_angles_rad_clipped)]
|
279
|
-
for i_redundancy, i_diag in enumerate(i_diag_list):
|
280
|
-
# print("IRED ", i_redundancy)
|
281
|
-
if i_redundancy:
|
282
|
-
# to avoid, in z_stages with >360 range for one single stage, to fill the second items which should instead be filled by another stage.
|
283
|
-
if abs(original_zpix_transl - self.diagnostic_zpix_transl[i_diag_list[0]]) < 2.0:
|
284
|
-
# print( " >>>>>> stesso z" , i_redundancy )
|
285
|
-
continue
|
286
|
-
|
287
|
-
if np.isnan(self.diagnostic_angles[i_diag]) or (
|
288
|
-
abs(original_angle) < abs(self.diagnostic_angles[i_diag] + safe_angular_margin)
|
289
|
-
):
|
290
|
-
# we are searching for the first contributions ( the one at the lowest angle)
|
291
|
-
# for the two diagnostics. With the constraint that the second is at an higher angle
|
292
|
-
# than the first. So if we are here this means that we have found an occurrence with
|
293
|
-
# lower angle and we discard what we could have previously found.
|
294
|
-
|
295
|
-
self.diagnostic_radios[i_diag][:] = 0
|
296
|
-
self.diagnostic_weights[i_diag][:] = 0
|
297
|
-
self.diagnostic_angles[i_diag] = original_angle
|
298
|
-
|
299
|
-
self.diagnostic_zpix_transl[i_diag] = original_zpix_transl
|
300
|
-
else:
|
301
|
-
continue
|
302
|
-
|
303
|
-
if abs(my_dist) <= my_angle_step_rad * 1.1:
|
304
|
-
factor = 1 - abs(my_dist) / (my_angle_step_rad)
|
305
|
-
|
306
|
-
self.diagnostic_radios[i_diag] += data_token * factor
|
307
|
-
self.diagnostic_weights[i_diag] += weight * factor
|
308
|
-
break
|
309
|
-
else:
|
310
|
-
pass
|
311
|
-
|
312
|
-
class _ReframingInfos:
|
313
|
-
def __init__(self, chunk_info, subchunk_slice, subr_start_end, dtasrc_start_end, subchunk_file_indexes):
|
314
|
-
self.subchunk_file_indexes = subchunk_file_indexes
|
315
|
-
my_integer_shifts_v = chunk_info.integer_shift_v[subchunk_slice]
|
316
|
-
self.fract_complement_shifts_v = chunk_info.fract_complement_to_integer_shift_v[subchunk_slice]
|
317
|
-
self.x_shifts_list = chunk_info.x_pix_per_proj[subchunk_slice]
|
318
|
-
subr_start_z, subr_end_z = subr_start_end
|
319
|
-
self.subr_start_z_list = subr_start_z - my_integer_shifts_v
|
320
|
-
self.subr_end_z_list = subr_end_z - my_integer_shifts_v + 1
|
321
|
-
|
322
|
-
self.dtasrc_start_z, self.dtasrc_end_z = dtasrc_start_end
|
323
|
-
|
324
|
-
floating_start_z = self.subr_start_z_list.min()
|
325
|
-
floating_end_z = self.subr_end_z_list.max()
|
326
|
-
|
327
|
-
self.floating_subregion = None, None, floating_start_z, floating_end_z
|
328
|
-
|
329
|
-
def _extract_preprocess_with_flats(
|
330
|
-
self, data_raw, reframing_infos, chunk_info, output, radios_angular_range_slicing=None, it_is_weight=False
|
331
|
-
):
|
332
|
-
if not it_is_weight:
|
333
|
-
if self.dark is not None:
|
334
|
-
data_raw = data_raw - self.dark[reframing_infos.dtasrc_start_z : reframing_infos.dtasrc_end_z]
|
335
|
-
|
336
|
-
if self.flats is not None:
|
337
|
-
for i, idx in enumerate(reframing_infos.subchunk_file_indexes):
|
338
|
-
flat = self._get_flat(idx, slice(reframing_infos.dtasrc_start_z, reframing_infos.dtasrc_end_z))
|
339
|
-
if self.dark is not None:
|
340
|
-
flat = flat - self.dark[reframing_infos.dtasrc_start_z : reframing_infos.dtasrc_end_z]
|
341
|
-
|
342
|
-
if self.radios_srcurrent is not None:
|
343
|
-
factor = self.nominal_current / self.radios_srcurrent[radios_angular_range_slicing.start + i]
|
344
|
-
else:
|
345
|
-
factor = 1
|
346
|
-
|
347
|
-
data_raw[i] = data_raw[i] * factor / flat
|
348
|
-
|
349
|
-
if self.double_flat is not None:
|
350
|
-
data_raw = data_raw / self.double_flat[reframing_infos.dtasrc_start_z : reframing_infos.dtasrc_end_z]
|
351
|
-
|
352
|
-
if it_is_weight:
|
353
|
-
# for the weight, the detector weights, depends on the detector portion,
|
354
|
-
# the one corresponding to dtasrc_start_end, and is the same across
|
355
|
-
# the subchunk first index ( the projection index)
|
356
|
-
take_data_from_this = [data_raw] * len(reframing_infos.subr_start_z_list)
|
357
|
-
else:
|
358
|
-
take_data_from_this = data_raw
|
359
|
-
|
360
|
-
for data_read, list_subr_start_z, list_subr_end_z, fract_shift, x_shift, data_target in zip(
|
361
|
-
take_data_from_this,
|
362
|
-
reframing_infos.subr_start_z_list,
|
363
|
-
reframing_infos.subr_end_z_list,
|
364
|
-
reframing_infos.fract_complement_shifts_v,
|
365
|
-
reframing_infos.x_shifts_list,
|
366
|
-
output,
|
367
|
-
):
|
368
|
-
_fill_in_chunk_by_shift_crop_data(
|
369
|
-
data_target,
|
370
|
-
data_read,
|
371
|
-
fract_shift,
|
372
|
-
list_subr_start_z,
|
373
|
-
list_subr_end_z,
|
374
|
-
reframing_infos.dtasrc_start_z,
|
375
|
-
reframing_infos.dtasrc_end_z,
|
376
|
-
x_shift=x_shift,
|
377
|
-
extension_padding=(not it_is_weight),
|
378
|
-
)
|
379
|
-
|
380
|
-
def _get_flat(self, idx, slice_y=slice(None, None), slice_x=slice(None, None), dtype=np.float32):
|
381
|
-
prev_next = FlatFieldArrays.get_previous_next_indices(self.flat_indexes, idx)
|
382
|
-
|
383
|
-
if len(prev_next) == 1: # current index corresponds to an acquired flat
|
384
|
-
flat_data = self.flats[self.flat_indexes_reverse_map[prev_next[0]]][slice_y, slice_x]
|
385
|
-
else: # interpolate
|
386
|
-
prev_idx, next_idx = prev_next
|
387
|
-
|
388
|
-
n_prev = self.flat_indexes_reverse_map[prev_idx]
|
389
|
-
n_next = self.flat_indexes_reverse_map[next_idx]
|
390
|
-
|
391
|
-
flat_data_prev = self.flats[n_prev][slice_y, slice_x]
|
392
|
-
flat_data_next = self.flats[n_next][slice_y, slice_x]
|
393
|
-
|
394
|
-
if self.flats_srcurrent is not None:
|
395
|
-
prev_current_factor = self.nominal_current / self.flats_srcurrent[n_prev]
|
396
|
-
next_current_factor = self.nominal_current / self.flats_srcurrent[n_next]
|
397
|
-
else:
|
398
|
-
prev_current_factor = 1
|
399
|
-
next_current_factor = 1
|
400
|
-
|
401
|
-
delta = next_idx - prev_idx
|
402
|
-
w1 = 1 - (idx - prev_idx) / delta
|
403
|
-
w2 = 1 - (next_idx - idx) / delta
|
404
|
-
|
405
|
-
if self.dark is not None:
|
406
|
-
dark = self.dark[slice_y, slice_x]
|
407
|
-
else:
|
408
|
-
dark = 0
|
409
|
-
|
410
|
-
flat_data = (
|
411
|
-
dark
|
412
|
-
+ w1 * (flat_data_prev - dark) * prev_current_factor
|
413
|
-
+ w2 * (flat_data_next - dark) * next_current_factor
|
414
|
-
)
|
415
|
-
|
416
|
-
if flat_data.dtype != dtype:
|
417
|
-
flat_data = np.ascontiguousarray(flat_data, dtype=dtype)
|
418
|
-
return flat_data
|
419
|
-
|
420
|
-
|
421
|
-
def _fill_in_chunk_by_shift_crop_data(
|
422
|
-
data_target,
|
423
|
-
data_read,
|
424
|
-
fract_shift,
|
425
|
-
my_subr_start_z,
|
426
|
-
my_subr_end_z,
|
427
|
-
dtasrc_start_z,
|
428
|
-
dtasrc_end_z,
|
429
|
-
x_shift=0.0,
|
430
|
-
extension_padding=True,
|
431
|
-
):
|
432
|
-
data_read_precisely_shifted = nd.shift(data_read, (-fract_shift, x_shift), order=1, mode="nearest")[:-1]
|
433
|
-
|
434
|
-
target_central_slicer, dtasrc_central_slicer = overlap_logic(
|
435
|
-
my_subr_start_z, my_subr_end_z - 1, dtasrc_start_z, dtasrc_end_z - 1
|
436
|
-
)
|
437
|
-
|
438
|
-
if None not in [target_central_slicer, dtasrc_central_slicer]:
|
439
|
-
data_target[target_central_slicer] = data_read_precisely_shifted[dtasrc_central_slicer]
|
440
|
-
|
441
|
-
target_lower_slicer, target_upper_slicer = padding_logic(
|
442
|
-
my_subr_start_z, my_subr_end_z - 1, dtasrc_start_z, dtasrc_end_z - 1
|
443
|
-
)
|
444
|
-
|
445
|
-
if extension_padding:
|
446
|
-
if target_lower_slicer is not None:
|
447
|
-
data_target[target_lower_slicer] = data_read_precisely_shifted[0]
|
448
|
-
if target_upper_slicer is not None:
|
449
|
-
data_target[target_upper_slicer] = data_read_precisely_shifted[-1]
|
450
|
-
else:
|
451
|
-
if target_lower_slicer is not None:
|
452
|
-
data_target[target_lower_slicer] = 1.0e-6
|
453
|
-
if target_upper_slicer is not None:
|
454
|
-
data_target[target_upper_slicer] = 1.0e-6
|
455
|
-
|
456
|
-
|
457
|
-
def overlap_logic(subr_start_z, subr_end_z, dtasrc_start_z, dtasrc_end_z):
|
458
|
-
"""determines the useful lines which can be transferred from the dtasrc_start_z:dtasrc_end_z
|
459
|
-
range targeting the range subr_start_z: subr_end_z ..................
|
460
|
-
|
461
|
-
"""
|
462
|
-
|
463
|
-
t_h = subr_end_z - subr_start_z
|
464
|
-
s_h = dtasrc_end_z - dtasrc_start_z
|
465
|
-
|
466
|
-
my_start = max(0, dtasrc_start_z - subr_start_z)
|
467
|
-
my_end = min(t_h, dtasrc_end_z - subr_start_z)
|
468
|
-
|
469
|
-
if my_start >= my_end:
|
470
|
-
return None, None
|
471
|
-
|
472
|
-
target_central_slicer = slice(my_start, my_end)
|
473
|
-
|
474
|
-
my_start = max(0, subr_start_z - dtasrc_start_z)
|
475
|
-
my_end = min(s_h, subr_end_z - dtasrc_start_z)
|
476
|
-
|
477
|
-
assert my_start < my_end, "Overlap_logic logic error"
|
478
|
-
|
479
|
-
dtasrc_central_slicer = slice(my_start, my_end)
|
480
|
-
|
481
|
-
return target_central_slicer, dtasrc_central_slicer
|
482
|
-
|
483
|
-
|
484
|
-
def padding_logic(subr_start_z, subr_end_z, dtasrc_start_z, dtasrc_end_z):
|
485
|
-
""".......... and the missing ranges which possibly could be obtained by extension padding"""
|
486
|
-
t_h = subr_end_z - subr_start_z
|
487
|
-
s_h = dtasrc_end_z - dtasrc_start_z
|
488
|
-
|
489
|
-
if dtasrc_start_z <= subr_start_z:
|
490
|
-
target_lower_padding = None
|
491
|
-
else:
|
492
|
-
target_lower_padding = slice(0, dtasrc_start_z - subr_start_z)
|
493
|
-
|
494
|
-
if dtasrc_end_z >= subr_end_z:
|
495
|
-
target_upper_padding = None
|
496
|
-
else:
|
497
|
-
target_upper_padding = slice(dtasrc_end_z - subr_end_z, None)
|
498
|
-
|
499
|
-
return target_lower_padding, target_upper_padding
|
500
|
-
|
501
|
-
|
502
|
-
def get_reconstruction_space(span_info, min_scanwise_z, end_scanwise_z, phase_margin_pix):
|
503
|
-
"""Utility function, so far used only by the unit test, which, given the span_info object, creates the auxiliary collection arrays
|
504
|
-
and initialises the my_z_min, my_z_end variable keeping into account the scan direction
|
505
|
-
and the min_scanwise_z, end_scanwise_z input arguments
|
506
|
-
Parameters
|
507
|
-
==========
|
508
|
-
|
509
|
-
span_info: SpanStrategy
|
510
|
-
|
511
|
-
min_scanwise_z: int
|
512
|
-
non negative number, where zero indicates the first feaseable slice doable scanwise.
|
513
|
-
Indicates the first (scanwise) requested slice to be reconstructed
|
514
|
-
|
515
|
-
end_scanwise_z: int
|
516
|
-
non negative number, where zero indicates the first feaseable slice doable scanwise.
|
517
|
-
Indicates the end (scanwise) slice which delimity the to be reconstructed requested slab.
|
518
|
-
|
519
|
-
"""
|
520
|
-
|
521
|
-
detector_z_start, detector_z_end = (span_info.get_doable_span()).view_heights_minmax
|
522
|
-
|
523
|
-
if span_info.z_pix_per_proj[-1] > span_info.z_pix_per_proj[0]:
|
524
|
-
my_z_min = detector_z_start + min_scanwise_z
|
525
|
-
my_z_end = detector_z_start + end_scanwise_z
|
526
|
-
else:
|
527
|
-
my_z_min = detector_z_end - (end_scanwise_z - 1)
|
528
|
-
my_z_end = detector_z_end - (min_scanwise_z + 1)
|
529
|
-
|
530
|
-
# while the raw dataset may have non uniform angular step
|
531
|
-
# the regridded dataset will have a constant step.
|
532
|
-
# We evaluate here below the number of angles for the
|
533
|
-
# regridded dataset, estimating a meaningul angular step representative
|
534
|
-
# of the raw data
|
535
|
-
my_angle_step = abs(np.diff(span_info.projection_angles_deg).mean())
|
536
|
-
n_gridded_angles = int(round(360.0 / my_angle_step))
|
537
|
-
|
538
|
-
radios_h = phase_margin_pix + (my_z_end - my_z_min) + phase_margin_pix
|
539
|
-
|
540
|
-
# the accumulators
|
541
|
-
gridded_radios = np.zeros([n_gridded_angles, radios_h, span_info.detector_shape_vh[1]], np.float32)
|
542
|
-
gridded_cumulated_weights = np.zeros([n_gridded_angles, radios_h, span_info.detector_shape_vh[1]], np.float32)
|
543
|
-
|
544
|
-
# this utility function is meant for testing the reconstruction only, not the diagnostic collection.
|
545
|
-
# However we build diagnostic targets all the same to feed something through the API
|
546
|
-
# which contemplates the diagnostics. So that the unit test runs correctly
|
547
|
-
|
548
|
-
diagnostic_radios = np.zeros((4,) + gridded_radios.shape[1:], np.float32)
|
549
|
-
diagnostic_weights = np.zeros((4,) + gridded_radios.shape[1:], np.float32)
|
550
|
-
diagnostic_proj_angle = np.zeros([4], "f")
|
551
|
-
|
552
|
-
diagnostic_searched_angles_rad_clipped = (0.5 + np.arange(2)) * (2 * np.pi / (2))
|
553
|
-
diagnostic_zpix_transl = np.zeros([4], "f")
|
554
|
-
|
555
|
-
gridded_angles_rad = np.arange(n_gridded_angles) * 2 * np.pi / n_gridded_angles
|
556
|
-
gridded_angles_deg = np.rad2deg(gridded_angles_rad)
|
557
|
-
|
558
|
-
res = type(
|
559
|
-
"on_the_fly_class_for_reconstruction_room_in_gridded_accumulator.py",
|
560
|
-
(object,),
|
561
|
-
{
|
562
|
-
"my_z_min": my_z_min,
|
563
|
-
"my_z_end": my_z_end,
|
564
|
-
"gridded_radios": gridded_radios,
|
565
|
-
"gridded_cumulated_weights": gridded_cumulated_weights,
|
566
|
-
"diagnostic_radios": diagnostic_radios,
|
567
|
-
"diagnostic_weights": diagnostic_weights,
|
568
|
-
"diagnostic_proj_angle": diagnostic_proj_angle,
|
569
|
-
"diagnostic_searched_angles_rad_clipped": diagnostic_searched_angles_rad_clipped,
|
570
|
-
"diagnostic_zpix_transl": diagnostic_zpix_transl,
|
571
|
-
"gridded_angles_rad": gridded_angles_rad,
|
572
|
-
"gridded_angles_deg": gridded_angles_deg,
|
573
|
-
},
|
574
|
-
)
|
575
|
-
return res
|