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_cuda.py +0 -53
- build/lib/nabu/processing/unsharp_opencl.py +0 -75
- build/lib/nabu/reconstruction/__init__.py +0 -3
- build/lib/nabu/reconstruction/cone.py +0 -241
- build/lib/nabu/reconstruction/fbp.py +0 -124
- build/lib/nabu/reconstruction/fbp_base.py +0 -391
- build/lib/nabu/reconstruction/fbp_opencl.py +0 -78
- build/lib/nabu/reconstruction/filtering.py +0 -220
- build/lib/nabu/reconstruction/filtering_cuda.py +0 -103
- build/lib/nabu/reconstruction/filtering_opencl.py +0 -111
- build/lib/nabu/reconstruction/projection.py +0 -240
- build/lib/nabu/reconstruction/reconstructor.py +0 -174
- build/lib/nabu/reconstruction/reconstructor_cuda.py +0 -44
- build/lib/nabu/reconstruction/rings.py +0 -248
- build/lib/nabu/reconstruction/rings_cuda.py +0 -322
- build/lib/nabu/reconstruction/sinogram.py +0 -467
- build/lib/nabu/reconstruction/sinogram_cuda.py +0 -250
- build/lib/nabu/reconstruction/sinogram_opencl.py +0 -40
- build/lib/nabu/reconstruction/tests/__init__.py +0 -1
- build/lib/nabu/reconstruction/tests/test_cone.py +0 -308
- build/lib/nabu/reconstruction/tests/test_deringer.py +0 -220
- build/lib/nabu/reconstruction/tests/test_fbp.py +0 -252
- build/lib/nabu/reconstruction/tests/test_filtering.py +0 -133
- build/lib/nabu/reconstruction/tests/test_halftomo.py +0 -100
- build/lib/nabu/reconstruction/tests/test_projector.py +0 -164
- build/lib/nabu/reconstruction/tests/test_reconstructor.py +0 -93
- build/lib/nabu/reconstruction/tests/test_sino_normalization.py +0 -85
- build/lib/nabu/resources/__init__.py +0 -0
- build/lib/nabu/resources/cli/__init__.py +0 -0
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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
- build/lib/nabu/resources/tests/test_units.py +0 -47
- build/lib/nabu/resources/utils.py +0 -174
- build/lib/nabu/stitching/__init__.py +0 -0
- build/lib/nabu/stitching/alignment.py +0 -184
- build/lib/nabu/stitching/config.py +0 -1286
- build/lib/nabu/stitching/definitions.py +0 -6
- build/lib/nabu/stitching/frame_composition.py +0 -155
- build/lib/nabu/stitching/overlap.py +0 -373
- build/lib/nabu/stitching/sample_normalization.py +0 -60
- build/lib/nabu/stitching/slurm_utils.py +0 -204
- build/lib/nabu/stitching/tests/__init__.py +0 -0
- build/lib/nabu/stitching/tests/test_alignment.py +0 -99
- build/lib/nabu/stitching/tests/test_config.py +0 -226
- build/lib/nabu/stitching/tests/test_frame_composition.py +0 -180
- build/lib/nabu/stitching/tests/test_overlap.py +0 -98
- build/lib/nabu/stitching/tests/test_sample_normalization.py +0 -49
- build/lib/nabu/stitching/tests/test_slurm_utils.py +0 -146
- build/lib/nabu/stitching/tests/test_utils.py +0 -21
- build/lib/nabu/stitching/tests/test_z_stitching.py +0 -1183
- build/lib/nabu/stitching/utils.py +0 -563
- build/lib/nabu/stitching/z_stitching.py +0 -2279
- build/lib/nabu/tests.py +0 -51
- build/lib/nabu/testutils.py +0 -375
- build/lib/nabu/thirdparty/__init__.py +0 -0
- build/lib/nabu/thirdparty/algotom_convert_sino.py +0 -276
- build/lib/nabu/thirdparty/pore3d_deringer_munch.py +0 -108
- build/lib/nabu/thirdparty/tomocupy_remove_stripe.py +0 -586
- build/lib/nabu/thirdparty/tomopy_phase.py +0 -239
- build/lib/nabu/thirdparty/tomwer_load_flats_darks.py +0 -162
- build/lib/nabu/utils.py +0 -836
- nabu-2024.1.1.dist-info/RECORD +0 -2375
- nabu-2024.1.1.dist-info/top_level.txt +0 -4
- {build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app → nabu/app/tests}/__init__.py +0 -0
- {nabu-2024.1.1.dist-info → nabu-2024.1.2.dist-info}/LICENSE +0 -0
- {nabu-2024.1.1.dist-info → nabu-2024.1.2.dist-info}/entry_points.txt +0 -0
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from ...resources.logger import LoggerOrPrint
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class SpanStrategy:
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def __init__(
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z_pix_per_proj,
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x_pix_per_proj,
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detector_shape_vh,
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phase_margin_pix,
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projection_angles_deg,
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logger=None,
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):
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"""
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This class does all the accounting for the reconstructible slices, giving for each one the list of the useful angles,
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of the vertical and horizontal shifts,and more ...
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Parameters
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----------
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z_pix_per_proj : array of floats
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an array of floats with one entry per projection, in pixel units. The values are the vertical displacements of the detector.
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In the experimental setup, the vertical detector axis is pointing toward the ground. Moreover the values are offsetted so that the
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first value is zero. The offset value, in millimiters is z_offset_mm and it is the vertical position of the sample stage relatively
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A z_pix=0 value indicates that the translation-rotation stage "ground" is exactly at the beam height ( supposed to be near the central line of the detector)
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plus z_offset_mm.
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A positive z_pix means that the translation stage has been lowered, compared to the first projection, in order to scan higher parts of the sample.
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( the sample is above the translation-rotation stage).
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x_pix_per_proj : array of floats
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one entry per projection. The horizontal displacement of the detector respect to the rotation axis.
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A positive x means that the sample shadow on the detector is moving toward the left of the detector.
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(the detector is going right)
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detector_shape_vh : a tuple of two ints
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the vertical and horizontal dimensions
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phase_margin_pix : int
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the maximum margin needed for the different kernels (phase, unsharp..) otherwhere in the pipeline
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projection_angles_deg : array of floats
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per each projection the rotation angle of the sample in degree.
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correction of the dead zones. The lines which do not satisfy this requirement are not doable.
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sample stage is below the detector for the first projection, and this is almost
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reconstruction informations according to several request formats: be they in
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sequential number of reconstructible slices, or millimeters above the stage.
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the criteria for deciding if a slice is reconstructable or not
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self.z_pix_per_proj = z_pix_per_proj
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self.phase_margin_pix = phase_margin_pix
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else:
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self.projection_angles_deg_internally = -projection_angles_deg
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self.angles_are_inverted = True
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self.projection_angles_deg = projection_angles_deg
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if (
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len(self.x_pix_per_proj) != self.total_num_images
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or len(self.projection_angles_deg_internally) != self.total_num_images
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):
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message = f"""
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all the arguments z_pix_per_proj, x_pix_per_proj and projection_angles_deg
|
96
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must have the same lenght but their lenght were
|
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{len(self.z_pix_per_proj) }, {len(self.x_pix_per_proj) }, {len(self.projection_angles_deg_internally) } respectively """
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raise ValueError(message)
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101
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## informations to be built are initialised to None here below
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""" For a given slice, the procedure for obtaining the useful angles, is based on the "sunshine" image,
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The sunshine image has two dimensions, the second one is the projection number
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while the first runs over the heights of the slices.
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All the logic is based on this image: when a given pixel of this image is zero, this corresponds
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to a pair (height,projection) for which there is no contribution of that projection to that slice.
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"""
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self.sunshine_image = None
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""" This will be an array of integer heights. We use a one-to-one correspondance beween these integers and slices
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in the reconstructed volume.
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The value of a given item is the vertical coordinate of an horizontal line in in the dectector
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(or above or below (negative values) ). More precisely the line over which the corresponding slice gets projected
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at the beginning of the scan ( in other words
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for the first vertical translation entry of the z_pix_per_proj argument)
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Illustratively, a view height equal to zero corresponds to
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a slice which projects on row 0 when translation is given by the first value in self.z_pix_per_proj.
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Negative integers for the heights are possible too, according to the direction of translations, which may bring
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above or below the detector. ( Illustratively
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the values in z_pix_per_proj are alway positive for the simple fact that the sample is above
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the roto-translation stage and the stage must be lowered in height for the beam to hit the sample.
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A scan starts always from a positive z_pix translation but the z_pix value may either decrease
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or increase. In fact for practical reasons, after having done a scan in one direction it is convenient to scan
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also while coming back after a previous scan)
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"""
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self.total_view_heights = None
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""" A list wich will contain for every reconstructable heigth, listed in self.total_view_heights, and in the same order,
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a pair of two integer, the first is the first sequential number of the projection for which the height is projected
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inside the detector, the second integer is the last projection number for which the projection occurs inside the detector.
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"""
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self.on_detector_projection_intervals = None
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""" All like self.on_detector_projection_intervals, but considering also the margins (phase, unsharp, etc).
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so that the height is projected inside the detector but while keeping
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a safe phase_margin_pix distance from the upper and lower border of the detector.
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"""
|
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self.within_margin_projection_intervals = None
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|
141
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""" This will contain projection number i_pro, the integer value given by
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ceil(z_pix_per_proj[i_pro])
|
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This array, together with the here below array self.fract_complement_to_integer_shift_v
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will be used for cropping when the data are collected for a given to be reconstructed chunk.
|
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"""
|
146
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self.integer_shift_v = np.zeros([self.total_num_images], "i")
|
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|
148
|
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""" The fractional vertical shifts are positive floats < 1.0 pixels.
|
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|
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This is the fractional part which, added to self.integer_shift_v,
|
150
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gives back z_pix_per_proj.
|
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Together with integer_shift_v, this array is meant to be used, by other modules, for cropping
|
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when the data are collected for a given to be reconstructed chunk."""
|
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self.fract_complement_to_integer_shift_v = np.zeros([self.total_num_images], "f")
|
154
|
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|
155
|
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self._setup_ephemerides()
|
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|
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|
157
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self._setup_sunshine()
|
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|
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|
159
|
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def get_doable_span(self):
|
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"""return an object with two properties:
|
161
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view_heights_minmax: containining minimum and maximum doable height ( detector reference at iproj=0)
|
162
|
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z_pix_minmax : containing minimum and maximum heights above the roto-translational sample stage
|
163
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"""
|
164
|
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vertical_profile = self.sunshine_image.sum(axis=1)
|
165
|
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|
166
|
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doable_indexes = np.arange(len(vertical_profile))[vertical_profile > 0]
|
167
|
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vertical_span = doable_indexes.min(), doable_indexes.max()
|
168
|
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|
169
|
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if not (vertical_profile[vertical_span[0] : vertical_span[1] + 1] > 0).all():
|
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message = """ Something wrong occurred in the span preprocessing.
|
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It appears that some intermetiade slices are not doables.
|
172
|
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The doable span should instead be contiguous. Please signal the problem"""
|
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raise RuntimeError(message)
|
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|
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|
175
|
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view_heights_minmax = self.total_view_heights[list(vertical_span)]
|
176
|
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|
177
|
-
hmin, hmax = view_heights_minmax
|
178
|
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d_v, d_h = self.detector_shape_vh
|
179
|
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z_min, z_max = (-self.z_pix_per_proj[0] + (d_v - 1) / 2 - hmax, -self.z_pix_per_proj[0] + (d_v - 1) / 2 - hmin)
|
180
|
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res = {
|
181
|
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"view_heights_minmax": view_heights_minmax,
|
182
|
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"z_pix_minmax": (z_min, z_max),
|
183
|
-
"z_mm_minmax": (z_min * self.pix_size_mm, z_max * self.pix_size_mm),
|
184
|
-
}
|
185
|
-
return DictToObj(res)
|
186
|
-
|
187
|
-
def get_informative_string(self):
|
188
|
-
doable_span_v = self.get_doable_span()
|
189
|
-
if self.z_pix_per_proj[-1] >= self.z_pix_per_proj[-1]:
|
190
|
-
direction = "ascending"
|
191
|
-
else:
|
192
|
-
direction = "descending"
|
193
|
-
|
194
|
-
s = f"""
|
195
|
-
Doable vertical span
|
196
|
-
--------------------
|
197
|
-
The scan has been performed with an {direction} vertical translation of the rotation axis.
|
198
|
-
|
199
|
-
The detector vertical axis is up side down.
|
200
|
-
|
201
|
-
Detector reference system at iproj=0:
|
202
|
-
from vertical view height ... {doable_span_v.view_heights_minmax[0]}
|
203
|
-
up to (included) ... {doable_span_v.view_heights_minmax[1]}
|
204
|
-
|
205
|
-
The slice that projects to the first line of the first projection
|
206
|
-
corresponds to vertical heigth = 0
|
207
|
-
|
208
|
-
In voxels, the vertical doable span measures: {doable_span_v.z_pix_minmax[1] - doable_span_v.z_pix_minmax[0]}
|
209
|
-
|
210
|
-
And in millimiters above the stage:
|
211
|
-
from vertical height above stage ( mm units) ... {doable_span_v.z_mm_minmax[0] - self.z_offset_mm }
|
212
|
-
up to (included) ... {doable_span_v.z_mm_minmax[1] - self.z_offset_mm }
|
213
|
-
"""
|
214
|
-
return s
|
215
|
-
|
216
|
-
def get_chunk_info(self, span_v_absolute):
|
217
|
-
"""
|
218
|
-
|
219
|
-
This method returns an object containing all the informations that are needed to reconstruct
|
220
|
-
the corresponding chunk
|
221
|
-
|
222
|
-
angle_index_span: a pair of integers indicating the start and the end of useful angles
|
223
|
-
in the array of all the scan angle self.projection_angles_deg
|
224
|
-
span_v: a pair of two integers indicating the start and end of the span relatively to the lowest value
|
225
|
-
of array self.total_view_heights
|
226
|
-
integer_shift_v: an array, containing for each one of the useful projections of the span,
|
227
|
-
the integer part of vertical shift to be used in cropping,
|
228
|
-
fract_complement_to_integer_shift_v :
|
229
|
-
the fractional remainder for cropping.
|
230
|
-
z_pix_per_proj: an array, containing for each to be used projection of the span
|
231
|
-
the vertical shift
|
232
|
-
x_pix_per_proj: ....the horizontal shit
|
233
|
-
angles_rad : an array, for each useful projection of the chunk the angle in radian
|
234
|
-
|
235
|
-
Parameters:
|
236
|
-
-----------
|
237
|
-
span_v_absolute: tuple of integers
|
238
|
-
a pair of two integers
|
239
|
-
the first view height ( referred to the detector y axis at iproj=0)
|
240
|
-
the second view height
|
241
|
-
with the first height smaller than the second.
|
242
|
-
"""
|
243
|
-
span_v = (span_v_absolute[0] - self.total_view_heights[0], span_v_absolute[1] - self.total_view_heights[0])
|
244
|
-
|
245
|
-
sunshine_subset = self.sunshine_image[span_v[0] : span_v[1]]
|
246
|
-
angular_profile = sunshine_subset.sum(axis=0)
|
247
|
-
|
248
|
-
angle_indexes = np.arange(len(self.projection_angles_deg_internally))[angular_profile > 0]
|
249
|
-
|
250
|
-
angle_index_span = angle_indexes.min(), angle_indexes.max() + 1
|
251
|
-
if not (np.less(0, angular_profile[angle_index_span[0] : angle_index_span[1]]).all()):
|
252
|
-
message = """ Something wrong occurred in the span preprocessing.
|
253
|
-
It appears that some intermediate slices are not doables.
|
254
|
-
The doable span should instead be contiguous. Please signal the problem"""
|
255
|
-
raise RuntimeError(message)
|
256
|
-
|
257
|
-
chunk_angles_deg = self.projection_angles_deg[angle_indexes]
|
258
|
-
|
259
|
-
my_slicer = slice(angle_index_span[0], angle_index_span[1])
|
260
|
-
values = (
|
261
|
-
angle_index_span,
|
262
|
-
span_v_absolute,
|
263
|
-
self.integer_shift_v[my_slicer],
|
264
|
-
self.fract_complement_to_integer_shift_v[my_slicer],
|
265
|
-
self.z_pix_per_proj[my_slicer],
|
266
|
-
self.x_pix_per_proj[my_slicer],
|
267
|
-
np.deg2rad(chunk_angles_deg) * (1 - 2 * int(self.angles_are_inverted)),
|
268
|
-
)
|
269
|
-
|
270
|
-
key_names = (
|
271
|
-
"angle_index_span",
|
272
|
-
"span_v",
|
273
|
-
"integer_shift_v",
|
274
|
-
"fract_complement_to_integer_shift_v",
|
275
|
-
"z_pix_per_proj",
|
276
|
-
"x_pix_per_proj",
|
277
|
-
"angles_rad",
|
278
|
-
)
|
279
|
-
|
280
|
-
return DictToObj(dict(zip(key_names, values)))
|
281
|
-
|
282
|
-
def _setup_ephemerides(self):
|
283
|
-
"""
|
284
|
-
A function which will set :
|
285
|
-
|
286
|
-
* self.integer_shift_v
|
287
|
-
* self.fract_complement_to_integer_shift_v
|
288
|
-
* self.total_view_heights
|
289
|
-
* self.on_detector_projection_intervals
|
290
|
-
* self.within_margin_projection_intervals
|
291
|
-
"""
|
292
|
-
|
293
|
-
for i_pro in range(self.total_num_images):
|
294
|
-
trans_v = self.z_pix_per_proj[i_pro]
|
295
|
-
self.integer_shift_v[i_pro] = math.ceil(trans_v)
|
296
|
-
self.fract_complement_to_integer_shift_v[i_pro] = math.ceil(trans_v) - trans_v
|
297
|
-
|
298
|
-
## The two following line initialize the view height, then considering the vertical translation
|
299
|
-
# the filed of view will be expanded
|
300
|
-
total_view_top = self.detector_shape_vh[0]
|
301
|
-
total_view_bottom = 0
|
302
|
-
|
303
|
-
total_view_top = max(total_view_top, int(math.ceil(total_view_top + self.z_pix_per_proj.max())))
|
304
|
-
total_view_bottom = min(total_view_bottom, int(math.floor(total_view_bottom + self.z_pix_per_proj.min())))
|
305
|
-
|
306
|
-
self.total_view_heights = np.arange(total_view_bottom, total_view_top + 1)
|
307
|
-
|
308
|
-
## where possible only data from within safe phase margin will be considered. (within_margin)
|
309
|
-
## if it is enough for 360 or more degree.
|
310
|
-
## If it is not enough we'll complete wih data close to the border, provided that data comes from within detector
|
311
|
-
## This will be
|
312
|
-
## the case for the first and last doable slices.
|
313
|
-
self.within_margin_projection_intervals = np.zeros(self.total_view_heights.shape + (2,), "i")
|
314
|
-
self.on_detector_projection_intervals = np.zeros(self.total_view_heights.shape + (2,), "i")
|
315
|
-
|
316
|
-
self.on_detector_projection_intervals[:, 1] = 0 # empty intervals
|
317
|
-
self.within_margin_projection_intervals[:, 1] = 0
|
318
|
-
|
319
|
-
for i_h, height in enumerate(self.total_view_heights):
|
320
|
-
previous_is_inside_detector = False
|
321
|
-
previous_is_inside_margin = False
|
322
|
-
|
323
|
-
pos_inside_filtered_v = height - self.integer_shift_v
|
324
|
-
|
325
|
-
is_inside_detector = np.less_equal(0, pos_inside_filtered_v)
|
326
|
-
is_inside_detector *= np.less(
|
327
|
-
pos_inside_filtered_v, self.detector_shape_vh[0] - np.less(0, self.fract_complement_to_integer_shift_v)
|
328
|
-
)
|
329
|
-
|
330
|
-
is_inside_margin = np.less_equal(self.phase_margin_pix, pos_inside_filtered_v)
|
331
|
-
is_inside_margin *= np.less(
|
332
|
-
pos_inside_filtered_v,
|
333
|
-
self.detector_shape_vh[0]
|
334
|
-
- self.phase_margin_pix
|
335
|
-
- np.less(0, self.fract_complement_to_integer_shift_v),
|
336
|
-
)
|
337
|
-
|
338
|
-
tmp = np.arange(self.total_num_images)[is_inside_detector]
|
339
|
-
if len(tmp):
|
340
|
-
self.on_detector_projection_intervals[i_h, :] = (tmp.min(), tmp.max())
|
341
|
-
|
342
|
-
tmp = np.arange(self.total_num_images)[is_inside_detector]
|
343
|
-
if len(tmp):
|
344
|
-
self.within_margin_projection_intervals[i_h, :] = (tmp.min(), tmp.max())
|
345
|
-
|
346
|
-
def _setup_sunshine(self):
|
347
|
-
"""It prepares
|
348
|
-
|
349
|
-
* self.sunshine_image
|
350
|
-
|
351
|
-
an image which for every height, contained in self.total_view_heights, and in the same order,
|
352
|
-
contains the list of factors, one per every projection of the total list. Each factor is a backprojection
|
353
|
-
weight. A non-doable height corresponds to a line full of zeros.
|
354
|
-
A doable height must correspond to a line having one and only one segment of contiguous non zero elements.
|
355
|
-
"""
|
356
|
-
|
357
|
-
self.sunshine_image = np.zeros(self.total_view_heights.shape + (self.total_num_images,), "f")
|
358
|
-
|
359
|
-
avg_angular_step_deg = np.diff(self.projection_angles_deg_internally).mean()
|
360
|
-
|
361
|
-
projection_angles_for_interp = np.concatenate(
|
362
|
-
[
|
363
|
-
[self.projection_angles_deg_internally[0] - avg_angular_step_deg],
|
364
|
-
self.projection_angles_deg_internally,
|
365
|
-
[self.projection_angles_deg_internally[-1] + avg_angular_step_deg],
|
366
|
-
]
|
367
|
-
)
|
368
|
-
|
369
|
-
data_container_for_interp = np.zeros_like(projection_angles_for_interp)
|
370
|
-
|
371
|
-
num_angular_periods = math.ceil(
|
372
|
-
(self.projection_angles_deg_internally.max() - self.projection_angles_deg_internally.min()) / 360
|
373
|
-
)
|
374
|
-
|
375
|
-
for i_h, height in enumerate(self.total_view_heights):
|
376
|
-
first_last_on_dect = self.on_detector_projection_intervals[i_h]
|
377
|
-
first_last_within_margin = self.within_margin_projection_intervals[i_h]
|
378
|
-
|
379
|
-
if first_last_on_dect[1] == 0:
|
380
|
-
# this line never entered in the fov
|
381
|
-
continue
|
382
|
-
|
383
|
-
angle_on_dect_first_last = self.projection_angles_deg_internally[first_last_on_dect]
|
384
|
-
angle_within_margin_first_last = self.projection_angles_deg_internally[first_last_within_margin]
|
385
|
-
|
386
|
-
# a mask which is positive for angular positions for which the height i_h gets projected within the detector
|
387
|
-
mask_on_dect = (
|
388
|
-
np.less_equal(angle_on_dect_first_last[0], self.projection_angles_deg_internally)
|
389
|
-
* np.less_equal(self.projection_angles_deg_internally, angle_on_dect_first_last[1])
|
390
|
-
).astype("f")
|
391
|
-
|
392
|
-
# a mask which is positive for angular positions for which the height i_h gets projected within the margins
|
393
|
-
mask_within_margin = (
|
394
|
-
np.less_equal(angle_within_margin_first_last[0], self.projection_angles_deg_internally)
|
395
|
-
* np.less_equal(self.projection_angles_deg_internally, angle_within_margin_first_last[1])
|
396
|
-
).astype("f")
|
397
|
-
|
398
|
-
## create a line which collects contributions from redundant angles
|
399
|
-
detector_collector = np.zeros(self.projection_angles_deg_internally.shape, "f")
|
400
|
-
margin_collector = np.zeros(self.projection_angles_deg_internally.shape, "f")
|
401
|
-
|
402
|
-
# the following loop tracks, for each projection, the total weight available at the projection angle
|
403
|
-
# The additional weight is coming from redundant angles.
|
404
|
-
# In this sense the sunshine_image implements a first rudimentary reweighting,
|
405
|
-
# which could be in principle used in the full pipeline, althought the regridded pipeline
|
406
|
-
# implements a, better, reweighting o its own.
|
407
|
-
for i_shift in range(-num_angular_periods, num_angular_periods + 1):
|
408
|
-
signus = (
|
409
|
-
1 if (self.projection_angles_deg_internally[-1] > self.projection_angles_deg_internally[0]) else -1
|
410
|
-
)
|
411
|
-
|
412
|
-
data_container_for_interp[1:-1] = mask_on_dect
|
413
|
-
|
414
|
-
detector_collector = detector_collector + mask_on_dect * np.interp(
|
415
|
-
(self.projection_angles_deg_internally + i_shift * 360) * signus,
|
416
|
-
signus * projection_angles_for_interp,
|
417
|
-
data_container_for_interp,
|
418
|
-
left=0,
|
419
|
-
right=0,
|
420
|
-
)
|
421
|
-
|
422
|
-
data_container_for_interp[1:-1] = mask_within_margin
|
423
|
-
|
424
|
-
margin_collector = margin_collector + mask_within_margin * np.interp(
|
425
|
-
(self.projection_angles_deg_internally + i_shift * 360) * signus,
|
426
|
-
signus * projection_angles_for_interp,
|
427
|
-
data_container_for_interp,
|
428
|
-
left=0,
|
429
|
-
right=0,
|
430
|
-
)
|
431
|
-
|
432
|
-
detector_shined_angles = self.projection_angles_deg_internally[detector_collector > 0.99]
|
433
|
-
margin_shined_angles = self.projection_angles_deg_internally[margin_collector > 0.99]
|
434
|
-
|
435
|
-
if not len(detector_shined_angles) > 1:
|
436
|
-
continue
|
437
|
-
|
438
|
-
avg_step_deg = abs(avg_angular_step_deg)
|
439
|
-
|
440
|
-
if len(margin_shined_angles):
|
441
|
-
angular_span_safe_margin = (
|
442
|
-
margin_shined_angles.max()
|
443
|
-
- margin_shined_angles.min()
|
444
|
-
+ avg_step_deg * (1.01 + self.angular_tolerance_steps)
|
445
|
-
)
|
446
|
-
else:
|
447
|
-
angular_span_safe_margin = 0
|
448
|
-
|
449
|
-
angular_span_bare_border = (
|
450
|
-
detector_shined_angles.max()
|
451
|
-
- detector_shined_angles.min()
|
452
|
-
+ avg_step_deg * (1.01 + self.angular_tolerance_steps)
|
453
|
-
)
|
454
|
-
|
455
|
-
if not self.require_redundancy:
|
456
|
-
if angular_span_safe_margin >= 360:
|
457
|
-
self.sunshine_image[i_h] = margin_collector
|
458
|
-
elif angular_span_bare_border >= 360:
|
459
|
-
self.sunshine_image[i_h] = detector_collector
|
460
|
-
else:
|
461
|
-
redundancy_angle_deg = 360
|
462
|
-
if angular_span_safe_margin >= 360 and angular_span_safe_margin > 2 * (
|
463
|
-
redundancy_angle_deg + avg_step_deg
|
464
|
-
):
|
465
|
-
self.sunshine_image[i_h] = margin_collector
|
466
|
-
elif angular_span_bare_border >= 360 and angular_span_bare_border > 2 * (
|
467
|
-
redundancy_angle_deg + avg_step_deg
|
468
|
-
):
|
469
|
-
self.sunshine_image[i_h] = detector_collector
|
470
|
-
|
471
|
-
sunshine_mask = np.less(0.99, self.sunshine_image)
|
472
|
-
|
473
|
-
self.sunshine_image[np.array([True]) ^ sunshine_mask] = 1.0
|
474
|
-
self.sunshine_image[:] = 1 / self.sunshine_image
|
475
|
-
self.sunshine_image[np.array([True]) ^ sunshine_mask] = 0.0
|
476
|
-
|
477
|
-
shp = self.sunshine_image.shape
|
478
|
-
X, Y = np.meshgrid(np.arange(shp[1]), np.arange(shp[0]))
|
479
|
-
|
480
|
-
condition = self.sunshine_image > 0
|
481
|
-
self.sunshine_starts = X.min(axis=1, initial=shp[1], where=condition)
|
482
|
-
self.sunshine_ends = X.max(axis=1, initial=0, where=condition)
|
483
|
-
self.sunshine_ends[self.sunshine_ends > 0] += 1
|
File without changes
|
@@ -1,157 +0,0 @@
|
|
1
|
-
from nabu.pipeline.helical import gridded_accumulator, span_strategy
|
2
|
-
from nabu.testutils import get_data
|
3
|
-
|
4
|
-
import pytest
|
5
|
-
import numpy as np
|
6
|
-
import os
|
7
|
-
import h5py
|
8
|
-
|
9
|
-
|
10
|
-
@pytest.fixture(scope="class")
|
11
|
-
def bootstrap(request):
|
12
|
-
cls = request.cls
|
13
|
-
|
14
|
-
# This is a helical dataset derived
|
15
|
-
# from "crayon" dataset, using 5 slices and covering 2.5 x 360 angular span
|
16
|
-
# in halftomo, with vertical translations.
|
17
|
-
|
18
|
-
helical_dataset = get_data("small_sparse_helical_dataset.npz")
|
19
|
-
|
20
|
-
helical_dataset = dict([item for item in helical_dataset.items()])
|
21
|
-
# the radios, in the dataset file, are stored by swapping angular and x dimension
|
22
|
-
# so that the fast running dimension runs over the projections.
|
23
|
-
# Due to the sparsity of the dataset, where only an handful of slices
|
24
|
-
# has signal, this gives a much better compression even when the axis is translating
|
25
|
-
# vertically
|
26
|
-
helical_dataset["radios"] = np.array(np.swapaxes(helical_dataset["radios_transposed"], 0, 2))
|
27
|
-
del helical_dataset["radios_transposed"]
|
28
|
-
|
29
|
-
# adding members: radios, dark, flats, z_pix_per_proj, x_pix_per_proj, projection_angles_deg, pixel_size_mm, phase_margin_pix,
|
30
|
-
# weigth_field=weigth_field, double_flat
|
31
|
-
dataset_keys = [
|
32
|
-
"dark",
|
33
|
-
"flats",
|
34
|
-
"z_pix_per_proj",
|
35
|
-
"x_pix_per_proj",
|
36
|
-
"projection_angles_deg",
|
37
|
-
"pixel_size_mm",
|
38
|
-
"phase_margin_pix",
|
39
|
-
"weights_field",
|
40
|
-
"double_flat",
|
41
|
-
"rotation_axis_position",
|
42
|
-
"detector_shape_vh",
|
43
|
-
"result_inset",
|
44
|
-
"radios",
|
45
|
-
]
|
46
|
-
for key in dataset_keys:
|
47
|
-
setattr(cls, key, helical_dataset[key])
|
48
|
-
|
49
|
-
cls.rtol_regridded = 1.0e-6
|
50
|
-
|
51
|
-
|
52
|
-
@pytest.mark.usefixtures("bootstrap")
|
53
|
-
class TestGriddedAccumulator:
|
54
|
-
"""
|
55
|
-
Test the GriddedAccumulator.
|
56
|
-
Rebuilds the sinogram for some selected slices of the crayon dataset
|
57
|
-
"""
|
58
|
-
|
59
|
-
def test_regridding(self):
|
60
|
-
span_info = span_strategy.SpanStrategy(
|
61
|
-
z_pix_per_proj=self.z_pix_per_proj,
|
62
|
-
x_pix_per_proj=self.x_pix_per_proj,
|
63
|
-
detector_shape_vh=self.detector_shape_vh,
|
64
|
-
phase_margin_pix=self.phase_margin_pix,
|
65
|
-
projection_angles_deg=self.projection_angles_deg,
|
66
|
-
require_redundancy=True,
|
67
|
-
pixel_size_mm=self.pixel_size_mm,
|
68
|
-
logger=None,
|
69
|
-
)
|
70
|
-
|
71
|
-
# I would like to reconstruct from feaseable height 15 to feaseable height 18
|
72
|
-
# relatively to the first doable slice in the vertical translation direction
|
73
|
-
# I get the heights in the detector frame of the first and of the last
|
74
|
-
|
75
|
-
reconstruction_space = gridded_accumulator.get_reconstruction_space(
|
76
|
-
span_info=span_info, min_scanwise_z=15, end_scanwise_z=18, phase_margin_pix=self.phase_margin_pix
|
77
|
-
)
|
78
|
-
|
79
|
-
chunk_info = span_info.get_chunk_info((reconstruction_space.my_z_min, reconstruction_space.my_z_end))
|
80
|
-
|
81
|
-
sub_region = (
|
82
|
-
reconstruction_space.my_z_min - self.phase_margin_pix,
|
83
|
-
reconstruction_space.my_z_end + self.phase_margin_pix,
|
84
|
-
)
|
85
|
-
|
86
|
-
## useful projections
|
87
|
-
proj_num_start, proj_num_end = chunk_info.angle_index_span
|
88
|
-
|
89
|
-
# the first of the chunk angular range
|
90
|
-
my_first_pnum = proj_num_start
|
91
|
-
|
92
|
-
self.accumulator = gridded_accumulator.GriddedAccumulator(
|
93
|
-
gridded_radios=reconstruction_space.gridded_radios,
|
94
|
-
gridded_weights=reconstruction_space.gridded_cumulated_weights,
|
95
|
-
diagnostic_radios=reconstruction_space.diagnostic_radios,
|
96
|
-
diagnostic_weights=reconstruction_space.diagnostic_weights,
|
97
|
-
diagnostic_angles=reconstruction_space.diagnostic_proj_angle,
|
98
|
-
diagnostic_searched_angles_rad_clipped=reconstruction_space.diagnostic_searched_angles_rad_clipped,
|
99
|
-
diagnostic_zpix_transl=reconstruction_space.diagnostic_zpix_transl,
|
100
|
-
dark=self.dark,
|
101
|
-
flat_indexes=[0, 7501],
|
102
|
-
flats=self.flats,
|
103
|
-
weights=self.weights_field,
|
104
|
-
double_flat=self.double_flat,
|
105
|
-
diag_zpro_run=0,
|
106
|
-
)
|
107
|
-
|
108
|
-
# splitting in sub ranges of 100 projections
|
109
|
-
n_granularity = 100
|
110
|
-
pnum_start_list = list(np.arange(proj_num_start, proj_num_end, n_granularity))
|
111
|
-
pnum_end_list = pnum_start_list[1:] + [proj_num_end]
|
112
|
-
|
113
|
-
for pnum_start, pnum_end in zip(pnum_start_list, pnum_end_list):
|
114
|
-
start_in_chunk = pnum_start - my_first_pnum
|
115
|
-
end_in_chunk = pnum_end - my_first_pnum
|
116
|
-
|
117
|
-
self._read_data_and_apply_flats(
|
118
|
-
slice(pnum_start, pnum_end), slice(start_in_chunk, end_in_chunk), chunk_info, sub_region, span_info
|
119
|
-
)
|
120
|
-
|
121
|
-
res = reconstruction_space.gridded_radios / reconstruction_space.gridded_cumulated_weights
|
122
|
-
|
123
|
-
# check only a sub part to avoid further increasing of the file on edna site
|
124
|
-
errmax = np.max(np.abs(res[:200, 1, -500:] - self.result_inset) / np.max(res))
|
125
|
-
assert errmax < self.rtol_regridded, "Max error is too high"
|
126
|
-
|
127
|
-
# uncomment this to see
|
128
|
-
# h5py.File("processed_sinogram.h5","w")["sinogram"] = res
|
129
|
-
|
130
|
-
def _read_data_and_apply_flats(self, sub_total_prange_slice, subchunk_slice, chunk_info, sub_region, span_info):
|
131
|
-
my_integer_shifts_v = chunk_info.integer_shift_v[subchunk_slice]
|
132
|
-
fract_complement_shifts_v = chunk_info.fract_complement_to_integer_shift_v[subchunk_slice]
|
133
|
-
x_shifts_list = chunk_info.x_pix_per_proj[subchunk_slice]
|
134
|
-
subr_start_z, subr_end_z = sub_region
|
135
|
-
|
136
|
-
subr_start_z_list = subr_start_z - my_integer_shifts_v
|
137
|
-
subr_end_z_list = subr_end_z - my_integer_shifts_v + 1
|
138
|
-
|
139
|
-
dtasrc_start_z = max(0, subr_start_z_list.min())
|
140
|
-
dtasrc_end_z = min(span_info.detector_shape_vh[0], subr_end_z_list.max())
|
141
|
-
|
142
|
-
data_raw = self.radios[sub_total_prange_slice, slice(dtasrc_start_z, dtasrc_end_z), :]
|
143
|
-
|
144
|
-
subsampling_file_slice = sub_total_prange_slice
|
145
|
-
|
146
|
-
# my_subsampled_indexes = self.chunk_reader._sorted_files_indices[subsampling_file_slice]
|
147
|
-
my_subsampled_indexes = (np.arange(10000))[subsampling_file_slice]
|
148
|
-
|
149
|
-
self.accumulator.extract_preprocess_with_flats(
|
150
|
-
subchunk_slice,
|
151
|
-
my_subsampled_indexes,
|
152
|
-
chunk_info,
|
153
|
-
np.array((subr_start_z, subr_end_z), "i"),
|
154
|
-
np.array((dtasrc_start_z, dtasrc_end_z), "i"),
|
155
|
-
data_raw,
|
156
|
-
sub_total_prange_slice,
|
157
|
-
)
|