nabu 2024.1.1__py3-none-any.whl → 2024.1.2__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- nabu/__init__.py +1 -1
- nabu/app/cast_volume.py +11 -2
- nabu/app/multicor.py +24 -2
- nabu/io/cast_volume.py +3 -3
- nabu/io/utils.py +2 -2
- nabu/stitching/tests/test_z_stitching.py +0 -1
- nabu/stitching/z_stitching.py +3 -3
- {nabu-2024.1.1.dist-info → nabu-2024.1.2.dist-info}/METADATA +2 -2
- nabu-2024.1.2.dist-info/RECORD +296 -0
- {nabu-2024.1.1.dist-info → nabu-2024.1.2.dist-info}/WHEEL +1 -1
- nabu-2024.1.2.dist-info/top_level.txt +2 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/doc/conf.py +0 -137
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/doc/create_conf_doc.py +0 -38
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/doc/get_mathjax.py +0 -34
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/__init__.py +0 -17
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/bootstrap.py +0 -88
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/bootstrap_stitching.py +0 -69
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/cast_volume.py +0 -272
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/cli_configs.py +0 -626
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/compare_volumes.py +0 -94
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/composite_cor.py +0 -144
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/correct_rot.py +0 -70
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/create_distortion_map_from_poly.py +0 -153
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/diag_to_pix.py +0 -358
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/diag_to_rot.py +0 -449
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/double_flatfield.py +0 -143
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/generate_header.py +0 -261
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/histogram.py +0 -197
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/multicor.py +0 -90
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/nx_z_splitter.py +0 -125
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/parse_reconstruction_log.py +0 -151
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/prepare_weights_double.py +0 -163
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/reconstruct.py +0 -120
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/reconstruct_helical.py +0 -116
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/reduce_dark_flat.py +0 -181
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/rotate.py +0 -162
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/shrink_dataset.py +0 -98
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/stitching.py +0 -85
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/tests/test_reduce_dark_flat.py +0 -78
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/utils.py +0 -33
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app/validator.py +0 -110
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/__init__.py +0 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/convolution.py +0 -8
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/fft.py +0 -4
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/kernel.py +0 -97
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/medfilt.py +0 -6
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/padding.py +0 -6
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/processing.py +0 -75
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/tests/__init__.py +0 -1
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/cuda/utils.py +0 -331
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/__init__.py +0 -12
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/alignment.py +0 -578
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/cor.py +0 -1621
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/cor_sino.py +0 -183
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/distortion.py +0 -112
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/focus.py +0 -362
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/__init__.py +0 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_alignment.py +0 -70
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_cor.py +0 -472
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_focus.py +0 -105
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_tilt.py +0 -41
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tests/test_translation.py +0 -78
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/tilt.py +0 -214
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/translation.py +0 -193
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/utils.py +0 -39
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/__init__.py +0 -2
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/cast_volume.py +0 -371
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/detector_distortion.py +0 -305
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/reader.py +0 -628
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/reader_helical.py +0 -114
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tests/__init__.py +0 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tests/test_cast_volume.py +0 -339
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tests/test_detector_distortion.py +0 -178
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tests/test_writers.py +0 -187
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/tiffwriter_zmm.py +0 -99
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/utils.py +0 -263
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/io/writer.py +0 -892
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/__init__.py +0 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/binning.py +0 -98
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/fftshift.py +0 -6
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/filters.py +0 -24
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/fourier_filters.py +0 -152
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/histogram.py +0 -6
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/histogram_cuda.py +0 -8
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/kernel_base.py +0 -4
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/padding.py +0 -83
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/padding_base.py +0 -6
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/processing_base.py +0 -4
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/rotation.py +0 -6
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/rotation_cuda.py +0 -6
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/tests/__init__.py +0 -1
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/tests/test_binning.py +0 -48
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/tests/test_interpolation.py +0 -70
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/transpose.py +0 -6
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/unsharp.py +0 -4
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/unsharp_cuda.py +0 -6
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/unsharp_opencl.py +0 -8
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/misc/utils.py +0 -117
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/__init__.py +0 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/fft.py +0 -6
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/kernel.py +0 -135
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/memcpy.py +0 -35
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/padding.py +0 -6
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/processing.py +0 -62
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/tests/__init__.py +0 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/opencl/utils.py +0 -292
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/__init__.py +0 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/config.py +0 -265
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/config_validators.py +0 -589
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/datadump.py +0 -164
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/dataset_validator.py +0 -211
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/detector_distortion_provider.py +0 -20
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/estimators.py +0 -1012
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fallback_utils.py +0 -149
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/__init__.py +0 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/chunked.py +0 -849
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/chunked_cuda.py +0 -152
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/computations.py +0 -260
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/dataset_validator.py +0 -63
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/nabu_config.py +0 -590
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/processconfig.py +0 -825
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/fullfield/reconstruction.py +0 -851
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/__init__.py +0 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/dataset_validator.py +0 -19
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/fbp.py +0 -147
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/filtering.py +0 -246
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/gridded_accumulator.py +0 -575
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_chunked_regridded.py +0 -1670
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_chunked_regridded_cuda.py +0 -119
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_reconstruction.py +0 -598
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/helical_utils.py +0 -42
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/nabu_config.py +0 -175
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/processconfig.py +0 -62
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/span_strategy.py +0 -483
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/__init__.py +0 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/test_accumulator.py +0 -157
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/test_pipeline_elements_full.py +0 -355
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/tests/test_strategy.py +0 -61
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/utils.py +0 -51
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/weight_balancer.py +0 -101
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/params.py +0 -163
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/processconfig.py +0 -210
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/tests/test_chunk_reader.py +0 -78
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/tests/test_estimators.py +0 -149
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/utils.py +0 -116
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/writer.py +0 -193
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/xrdct/__init__.py +0 -0
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/__init__.py +0 -7
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/alignment.py +0 -11
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ccd.py +0 -161
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ccd_cuda.py +0 -169
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ctf.py +0 -361
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/ctf_cuda.py +0 -142
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/distortion.py +0 -92
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/double_flatfield.py +0 -212
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/double_flatfield_cuda.py +0 -174
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/double_flatfield_variable_region.py +0 -68
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/flatfield.py +0 -448
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/flatfield_cuda.py +0 -144
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/flatfield_variable_region.py +0 -79
- build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/phase.py +0 -425
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- build/lib/nabu/app/nx_z_splitter.py +0 -125
- build/lib/nabu/app/parse_reconstruction_log.py +0 -151
- build/lib/nabu/app/prepare_weights_double.py +0 -163
- build/lib/nabu/app/reconstruct.py +0 -120
- build/lib/nabu/app/reconstruct_helical.py +0 -116
- build/lib/nabu/app/reduce_dark_flat.py +0 -181
- build/lib/nabu/app/rotate.py +0 -162
- build/lib/nabu/app/shrink_dataset.py +0 -98
- build/lib/nabu/app/stitching.py +0 -85
- build/lib/nabu/app/tests/test_reduce_dark_flat.py +0 -78
- build/lib/nabu/app/utils.py +0 -33
- build/lib/nabu/app/validator.py +0 -110
- build/lib/nabu/cuda/__init__.py +0 -0
- build/lib/nabu/cuda/convolution.py +0 -8
- build/lib/nabu/cuda/fft.py +0 -4
- build/lib/nabu/cuda/kernel.py +0 -97
- build/lib/nabu/cuda/medfilt.py +0 -6
- build/lib/nabu/cuda/padding.py +0 -6
- build/lib/nabu/cuda/processing.py +0 -75
- build/lib/nabu/cuda/tests/__init__.py +0 -1
- build/lib/nabu/cuda/utils.py +0 -331
- build/lib/nabu/estimation/__init__.py +0 -12
- build/lib/nabu/estimation/alignment.py +0 -578
- build/lib/nabu/estimation/cor.py +0 -1621
- build/lib/nabu/estimation/cor_sino.py +0 -183
- build/lib/nabu/estimation/distortion.py +0 -112
- build/lib/nabu/estimation/focus.py +0 -362
- build/lib/nabu/estimation/tests/__init__.py +0 -0
- build/lib/nabu/estimation/tests/test_alignment.py +0 -70
- build/lib/nabu/estimation/tests/test_cor.py +0 -472
- build/lib/nabu/estimation/tests/test_focus.py +0 -105
- build/lib/nabu/estimation/tests/test_tilt.py +0 -41
- build/lib/nabu/estimation/tests/test_translation.py +0 -78
- build/lib/nabu/estimation/tilt.py +0 -214
- build/lib/nabu/estimation/translation.py +0 -193
- build/lib/nabu/estimation/utils.py +0 -39
- build/lib/nabu/io/__init__.py +0 -2
- build/lib/nabu/io/cast_volume.py +0 -371
- build/lib/nabu/io/detector_distortion.py +0 -305
- build/lib/nabu/io/reader.py +0 -628
- build/lib/nabu/io/reader_helical.py +0 -114
- build/lib/nabu/io/tests/__init__.py +0 -0
- build/lib/nabu/io/tests/test_cast_volume.py +0 -339
- build/lib/nabu/io/tests/test_detector_distortion.py +0 -178
- build/lib/nabu/io/tests/test_writers.py +0 -187
- build/lib/nabu/io/tiffwriter_zmm.py +0 -99
- build/lib/nabu/io/utils.py +0 -263
- build/lib/nabu/io/writer.py +0 -892
- build/lib/nabu/misc/__init__.py +0 -0
- build/lib/nabu/misc/binning.py +0 -98
- build/lib/nabu/misc/fftshift.py +0 -6
- build/lib/nabu/misc/filters.py +0 -24
- build/lib/nabu/misc/fourier_filters.py +0 -152
- build/lib/nabu/misc/histogram.py +0 -6
- build/lib/nabu/misc/histogram_cuda.py +0 -8
- build/lib/nabu/misc/kernel_base.py +0 -4
- build/lib/nabu/misc/padding.py +0 -83
- build/lib/nabu/misc/padding_base.py +0 -6
- build/lib/nabu/misc/processing_base.py +0 -4
- build/lib/nabu/misc/rotation.py +0 -6
- build/lib/nabu/misc/rotation_cuda.py +0 -6
- build/lib/nabu/misc/tests/__init__.py +0 -1
- build/lib/nabu/misc/tests/test_binning.py +0 -48
- build/lib/nabu/misc/tests/test_interpolation.py +0 -70
- build/lib/nabu/misc/transpose.py +0 -6
- build/lib/nabu/misc/unsharp.py +0 -4
- build/lib/nabu/misc/unsharp_cuda.py +0 -6
- build/lib/nabu/misc/unsharp_opencl.py +0 -8
- build/lib/nabu/misc/utils.py +0 -117
- build/lib/nabu/opencl/__init__.py +0 -0
- build/lib/nabu/opencl/fft.py +0 -6
- build/lib/nabu/opencl/kernel.py +0 -135
- build/lib/nabu/opencl/memcpy.py +0 -35
- build/lib/nabu/opencl/padding.py +0 -6
- build/lib/nabu/opencl/processing.py +0 -62
- build/lib/nabu/opencl/tests/__init__.py +0 -0
- build/lib/nabu/opencl/utils.py +0 -292
- build/lib/nabu/pipeline/__init__.py +0 -0
- build/lib/nabu/pipeline/config.py +0 -265
- build/lib/nabu/pipeline/config_validators.py +0 -589
- build/lib/nabu/pipeline/datadump.py +0 -164
- build/lib/nabu/pipeline/dataset_validator.py +0 -211
- build/lib/nabu/pipeline/detector_distortion_provider.py +0 -20
- build/lib/nabu/pipeline/estimators.py +0 -1012
- build/lib/nabu/pipeline/fallback_utils.py +0 -149
- build/lib/nabu/pipeline/fullfield/__init__.py +0 -0
- build/lib/nabu/pipeline/fullfield/chunked.py +0 -849
- build/lib/nabu/pipeline/fullfield/chunked_cuda.py +0 -152
- build/lib/nabu/pipeline/fullfield/computations.py +0 -260
- build/lib/nabu/pipeline/fullfield/dataset_validator.py +0 -63
- build/lib/nabu/pipeline/fullfield/nabu_config.py +0 -590
- build/lib/nabu/pipeline/fullfield/processconfig.py +0 -825
- build/lib/nabu/pipeline/fullfield/reconstruction.py +0 -851
- build/lib/nabu/pipeline/helical/__init__.py +0 -0
- build/lib/nabu/pipeline/helical/dataset_validator.py +0 -19
- build/lib/nabu/pipeline/helical/fbp.py +0 -147
- build/lib/nabu/pipeline/helical/filtering.py +0 -246
- build/lib/nabu/pipeline/helical/gridded_accumulator.py +0 -575
- build/lib/nabu/pipeline/helical/helical_chunked_regridded.py +0 -1670
- build/lib/nabu/pipeline/helical/helical_chunked_regridded_cuda.py +0 -119
- build/lib/nabu/pipeline/helical/helical_reconstruction.py +0 -598
- build/lib/nabu/pipeline/helical/helical_utils.py +0 -42
- build/lib/nabu/pipeline/helical/nabu_config.py +0 -175
- build/lib/nabu/pipeline/helical/processconfig.py +0 -62
- build/lib/nabu/pipeline/helical/span_strategy.py +0 -483
- build/lib/nabu/pipeline/helical/tests/__init__.py +0 -0
- build/lib/nabu/pipeline/helical/tests/test_accumulator.py +0 -157
- build/lib/nabu/pipeline/helical/tests/test_pipeline_elements_full.py +0 -355
- build/lib/nabu/pipeline/helical/tests/test_strategy.py +0 -61
- build/lib/nabu/pipeline/helical/utils.py +0 -51
- build/lib/nabu/pipeline/helical/weight_balancer.py +0 -101
- build/lib/nabu/pipeline/params.py +0 -163
- build/lib/nabu/pipeline/processconfig.py +0 -210
- build/lib/nabu/pipeline/tests/test_chunk_reader.py +0 -78
- build/lib/nabu/pipeline/tests/test_estimators.py +0 -149
- build/lib/nabu/pipeline/utils.py +0 -116
- build/lib/nabu/pipeline/writer.py +0 -193
- build/lib/nabu/pipeline/xrdct/__init__.py +0 -0
- build/lib/nabu/preproc/__init__.py +0 -7
- build/lib/nabu/preproc/alignment.py +0 -11
- build/lib/nabu/preproc/ccd.py +0 -161
- build/lib/nabu/preproc/ccd_cuda.py +0 -169
- build/lib/nabu/preproc/ctf.py +0 -361
- build/lib/nabu/preproc/ctf_cuda.py +0 -142
- build/lib/nabu/preproc/distortion.py +0 -92
- build/lib/nabu/preproc/double_flatfield.py +0 -212
- build/lib/nabu/preproc/double_flatfield_cuda.py +0 -174
- build/lib/nabu/preproc/double_flatfield_variable_region.py +0 -68
- build/lib/nabu/preproc/flatfield.py +0 -448
- build/lib/nabu/preproc/flatfield_cuda.py +0 -144
- build/lib/nabu/preproc/flatfield_variable_region.py +0 -79
- build/lib/nabu/preproc/phase.py +0 -425
- build/lib/nabu/preproc/phase_cuda.py +0 -143
- build/lib/nabu/preproc/shift.py +0 -95
- build/lib/nabu/preproc/shift_cuda.py +0 -102
- build/lib/nabu/preproc/tests/__init__.py +0 -1
- build/lib/nabu/preproc/tests/test_ccd_corr.py +0 -59
- build/lib/nabu/preproc/tests/test_ctf.py +0 -250
- build/lib/nabu/preproc/tests/test_double_flatfield.py +0 -86
- build/lib/nabu/preproc/tests/test_flatfield.py +0 -626
- build/lib/nabu/preproc/tests/test_paganin.py +0 -67
- build/lib/nabu/preproc/tests/test_vshift.py +0 -73
- build/lib/nabu/processing/__init__.py +0 -0
- build/lib/nabu/processing/convolution_cuda.py +0 -375
- build/lib/nabu/processing/fft_base.py +0 -163
- build/lib/nabu/processing/fft_cuda.py +0 -256
- build/lib/nabu/processing/fft_opencl.py +0 -54
- build/lib/nabu/processing/fftshift.py +0 -134
- build/lib/nabu/processing/histogram.py +0 -286
- build/lib/nabu/processing/histogram_cuda.py +0 -103
- build/lib/nabu/processing/kernel_base.py +0 -126
- build/lib/nabu/processing/medfilt_cuda.py +0 -159
- build/lib/nabu/processing/muladd.py +0 -29
- build/lib/nabu/processing/muladd_cuda.py +0 -68
- build/lib/nabu/processing/padding_base.py +0 -71
- build/lib/nabu/processing/padding_cuda.py +0 -75
- build/lib/nabu/processing/padding_opencl.py +0 -77
- build/lib/nabu/processing/processing_base.py +0 -123
- build/lib/nabu/processing/roll_opencl.py +0 -64
- build/lib/nabu/processing/rotation.py +0 -63
- build/lib/nabu/processing/rotation_cuda.py +0 -66
- build/lib/nabu/processing/tests/__init__.py +0 -0
- build/lib/nabu/processing/tests/test_fft.py +0 -268
- build/lib/nabu/processing/tests/test_fftshift.py +0 -71
- build/lib/nabu/processing/tests/test_histogram.py +0 -55
- build/lib/nabu/processing/tests/test_medfilt.py +0 -77
- build/lib/nabu/processing/tests/test_muladd.py +0 -54
- build/lib/nabu/processing/tests/test_padding.py +0 -247
- build/lib/nabu/processing/tests/test_roll.py +0 -63
- build/lib/nabu/processing/tests/test_rotation.py +0 -83
- build/lib/nabu/processing/tests/test_transpose.py +0 -72
- build/lib/nabu/processing/tests/test_unsharp.py +0 -106
- build/lib/nabu/processing/transpose.py +0 -126
- build/lib/nabu/processing/unsharp.py +0 -79
- build/lib/nabu/processing/unsharp_cuda.py +0 -53
- build/lib/nabu/processing/unsharp_opencl.py +0 -75
- build/lib/nabu/reconstruction/__init__.py +0 -3
- build/lib/nabu/reconstruction/cone.py +0 -241
- build/lib/nabu/reconstruction/fbp.py +0 -124
- build/lib/nabu/reconstruction/fbp_base.py +0 -391
- build/lib/nabu/reconstruction/fbp_opencl.py +0 -78
- build/lib/nabu/reconstruction/filtering.py +0 -220
- build/lib/nabu/reconstruction/filtering_cuda.py +0 -103
- build/lib/nabu/reconstruction/filtering_opencl.py +0 -111
- build/lib/nabu/reconstruction/projection.py +0 -240
- build/lib/nabu/reconstruction/reconstructor.py +0 -174
- build/lib/nabu/reconstruction/reconstructor_cuda.py +0 -44
- build/lib/nabu/reconstruction/rings.py +0 -248
- build/lib/nabu/reconstruction/rings_cuda.py +0 -322
- build/lib/nabu/reconstruction/sinogram.py +0 -467
- build/lib/nabu/reconstruction/sinogram_cuda.py +0 -250
- build/lib/nabu/reconstruction/sinogram_opencl.py +0 -40
- build/lib/nabu/reconstruction/tests/__init__.py +0 -1
- build/lib/nabu/reconstruction/tests/test_cone.py +0 -308
- build/lib/nabu/reconstruction/tests/test_deringer.py +0 -220
- build/lib/nabu/reconstruction/tests/test_fbp.py +0 -252
- build/lib/nabu/reconstruction/tests/test_filtering.py +0 -133
- build/lib/nabu/reconstruction/tests/test_halftomo.py +0 -100
- build/lib/nabu/reconstruction/tests/test_projector.py +0 -164
- build/lib/nabu/reconstruction/tests/test_reconstructor.py +0 -93
- build/lib/nabu/reconstruction/tests/test_sino_normalization.py +0 -85
- build/lib/nabu/resources/__init__.py +0 -0
- build/lib/nabu/resources/cli/__init__.py +0 -0
- build/lib/nabu/resources/cor.py +0 -5
- build/lib/nabu/resources/dataset_analyzer.py +0 -469
- build/lib/nabu/resources/gpu.py +0 -169
- build/lib/nabu/resources/logger.py +0 -130
- build/lib/nabu/resources/nxflatfield.py +0 -217
- build/lib/nabu/resources/templates/__init__.py +0 -0
- build/lib/nabu/resources/tests/__init__.py +0 -0
- build/lib/nabu/resources/tests/test_nxflatfield.py +0 -104
- build/lib/nabu/resources/tests/test_units.py +0 -47
- build/lib/nabu/resources/utils.py +0 -174
- build/lib/nabu/stitching/__init__.py +0 -0
- build/lib/nabu/stitching/alignment.py +0 -184
- build/lib/nabu/stitching/config.py +0 -1286
- build/lib/nabu/stitching/definitions.py +0 -6
- build/lib/nabu/stitching/frame_composition.py +0 -155
- build/lib/nabu/stitching/overlap.py +0 -373
- build/lib/nabu/stitching/sample_normalization.py +0 -60
- build/lib/nabu/stitching/slurm_utils.py +0 -204
- build/lib/nabu/stitching/tests/__init__.py +0 -0
- build/lib/nabu/stitching/tests/test_alignment.py +0 -99
- build/lib/nabu/stitching/tests/test_config.py +0 -226
- build/lib/nabu/stitching/tests/test_frame_composition.py +0 -180
- build/lib/nabu/stitching/tests/test_overlap.py +0 -98
- build/lib/nabu/stitching/tests/test_sample_normalization.py +0 -49
- build/lib/nabu/stitching/tests/test_slurm_utils.py +0 -146
- build/lib/nabu/stitching/tests/test_utils.py +0 -21
- build/lib/nabu/stitching/tests/test_z_stitching.py +0 -1183
- build/lib/nabu/stitching/utils.py +0 -563
- build/lib/nabu/stitching/z_stitching.py +0 -2279
- build/lib/nabu/tests.py +0 -51
- build/lib/nabu/testutils.py +0 -375
- build/lib/nabu/thirdparty/__init__.py +0 -0
- build/lib/nabu/thirdparty/algotom_convert_sino.py +0 -276
- build/lib/nabu/thirdparty/pore3d_deringer_munch.py +0 -108
- build/lib/nabu/thirdparty/tomocupy_remove_stripe.py +0 -586
- build/lib/nabu/thirdparty/tomopy_phase.py +0 -239
- build/lib/nabu/thirdparty/tomwer_load_flats_darks.py +0 -162
- build/lib/nabu/utils.py +0 -836
- nabu-2024.1.1.dist-info/RECORD +0 -2375
- nabu-2024.1.1.dist-info/top_level.txt +0 -4
- {build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/app → nabu/app/tests}/__init__.py +0 -0
- {nabu-2024.1.1.dist-info → nabu-2024.1.2.dist-info}/LICENSE +0 -0
- {nabu-2024.1.1.dist-info → nabu-2024.1.2.dist-info}/entry_points.txt +0 -0
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scenarios = [{key: val for key, val in zip(configurations.keys(), p_)} for p_ in product(*configurations.values())]
|
48
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return scenarios
|
49
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|
50
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-
|
51
|
-
def get_data(*dataset_path):
|
52
|
-
"""
|
53
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-
Get a dataset file from silx.org/pub/nabu/data
|
54
|
-
dataset_args is a list describing a nested folder structures, ex.
|
55
|
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["path", "to", "my", "dataset.h5"]
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56
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-
"""
|
57
|
-
dataset_relpath = os.path.join(*dataset_path)
|
58
|
-
dataset_downloaded_path = utilstest.getfile(dataset_relpath)
|
59
|
-
return np.load(dataset_downloaded_path)
|
60
|
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|
61
|
-
|
62
|
-
def get_array_of_given_shape(img, shape, dtype):
|
63
|
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"""
|
64
|
-
From a given image, returns an array of the wanted shape and dtype.
|
65
|
-
"""
|
66
|
-
|
67
|
-
# Tile image until it's big enough.
|
68
|
-
# "fun" fact: using any(blabla) crashes but using any([blabla]) does not, because of variables re-evaluation
|
69
|
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while any([i_dim <= s_dim for i_dim, s_dim in zip(img.shape, shape)]):
|
70
|
-
img = np.tile(img, (2, 2))
|
71
|
-
if len(shape) == 1:
|
72
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-
arr = img[: shape[0], 0]
|
73
|
-
elif len(shape) == 2:
|
74
|
-
arr = img[: shape[0], : shape[1]]
|
75
|
-
else:
|
76
|
-
arr = np.tile(img, (shape[0], 1, 1))[: shape[0], : shape[1], : shape[2]]
|
77
|
-
return np.ascontiguousarray(np.squeeze(arr), dtype=dtype)
|
78
|
-
|
79
|
-
|
80
|
-
def get_big_data(filename):
|
81
|
-
if __big_testdata_dir__ is None:
|
82
|
-
return None
|
83
|
-
return np.load(os.path.join(__big_testdata_dir__, filename))
|
84
|
-
|
85
|
-
|
86
|
-
def uncompress_file(compressed_file_path, target_directory):
|
87
|
-
with tarfile.open(compressed_file_path) as f:
|
88
|
-
f.extractall(path=target_directory)
|
89
|
-
|
90
|
-
|
91
|
-
def get_file(fname):
|
92
|
-
downloaded_file = dataset_downloaded_path = utilstest.getfile(fname)
|
93
|
-
if ".tar" in fname:
|
94
|
-
uncompress_file(downloaded_file, os.path.dirname(downloaded_file))
|
95
|
-
downloaded_file = downloaded_file.split(".tar")[0]
|
96
|
-
return downloaded_file
|
97
|
-
|
98
|
-
|
99
|
-
def compare_arrays(arr1, arr2, tol, diff=None, absolute_value=True, percent=None, method="max", return_residual=False):
|
100
|
-
"""
|
101
|
-
Utility to compare two arrays.
|
102
|
-
|
103
|
-
Parameters
|
104
|
-
----------
|
105
|
-
arr1: numpy.ndarray
|
106
|
-
First array to compare
|
107
|
-
arr2: numpy.ndarray
|
108
|
-
Second array to compare
|
109
|
-
tol: float
|
110
|
-
Tolerance indicating whether arrays are close to eachother.
|
111
|
-
diff: numpy.ndarray, optional
|
112
|
-
Difference `arr1 - arr2`. If provided, this array is taken instead of `arr1`
|
113
|
-
and `arr2`.
|
114
|
-
absolute_value: bool, optional
|
115
|
-
Whether to take absolute value of the difference.
|
116
|
-
percent: float
|
117
|
-
If set, a "relative" comparison is performed instead of a subtraction:
|
118
|
-
`red(|arr1 - arr2|) / (red(|arr1|) * percent) < tol`
|
119
|
-
where "red" is the reduction method (mean, max or median).
|
120
|
-
method:
|
121
|
-
Reduction method. Can be "max", "mean", or "median".
|
122
|
-
|
123
|
-
Returns
|
124
|
-
--------
|
125
|
-
(is_close, residual) if return_residual is set to True
|
126
|
-
is_close otherwise
|
127
|
-
|
128
|
-
Examples
|
129
|
-
--------
|
130
|
-
When using method="mean" and absolute_value=True, this function computes
|
131
|
-
the Mean Absolute Difference (MAD) metric.
|
132
|
-
When also using percent=1.0, this computes the Relative Mean Absolute Difference
|
133
|
-
(RMD) metric.
|
134
|
-
"""
|
135
|
-
reductions = {
|
136
|
-
"max": np.max,
|
137
|
-
"mean": np.mean,
|
138
|
-
"median": np.median,
|
139
|
-
}
|
140
|
-
if method not in reductions:
|
141
|
-
raise ValueError("reduction method should be in %s" % str(list(reductions.keys())))
|
142
|
-
if diff is None:
|
143
|
-
diff = arr1 - arr2
|
144
|
-
if absolute_value is not None:
|
145
|
-
diff = np.abs(diff)
|
146
|
-
residual = reductions[method](diff)
|
147
|
-
if percent is not None:
|
148
|
-
a1 = np.abs(arr1) if absolute_value else arr1
|
149
|
-
residual /= reductions[method](a1)
|
150
|
-
|
151
|
-
res = residual < tol
|
152
|
-
if return_residual:
|
153
|
-
res = res, residual
|
154
|
-
return res
|
155
|
-
|
156
|
-
|
157
|
-
def gaussian_apodization_window(shape, fwhm_ratio=0.7):
|
158
|
-
fwhm = fwhm_ratio * np.array(shape)
|
159
|
-
sigma = fwhm / 2.355
|
160
|
-
return np.outer(*[gaussian(n, s) for n, s in zip(shape, sigma)])
|
161
|
-
|
162
|
-
|
163
|
-
def compare_shifted_images(img1, img2, fwhm_ratio=0.7, return_upper_bound=False):
|
164
|
-
"""
|
165
|
-
Compare two images that are slightly shifted from one another.
|
166
|
-
Typically, tomography reconstruction wight slightly different CoR.
|
167
|
-
Each image is Fourier-transformed, and the modulus is taken to get rid of the shift between the images.
|
168
|
-
An apodization is done to filter the high frequencies that are usually less relevant.
|
169
|
-
|
170
|
-
Parameters
|
171
|
-
----------
|
172
|
-
img1: numpy.ndarray
|
173
|
-
First image
|
174
|
-
img2: numpy.ndarray
|
175
|
-
Second image
|
176
|
-
fwhm_ratio: float, optional
|
177
|
-
Ratio defining the apodization in the frequency domain.
|
178
|
-
A small value (eg. 0.2) means that essentually only the low frequencies will be compared.
|
179
|
-
A value of 1.0 means no apodization
|
180
|
-
return_upper_bound: bool, optional
|
181
|
-
Whether to return a (coarse) upper bound of the comparison metric
|
182
|
-
|
183
|
-
Notes
|
184
|
-
-----
|
185
|
-
This function roughly computes
|
186
|
-
|phi(F(img1)) - phi(F(img2))|
|
187
|
-
where F is the absolute value of the Fourier transform, and phi some shrinking function (here arcsinh).
|
188
|
-
"""
|
189
|
-
|
190
|
-
def _fourier_transform(img):
|
191
|
-
return np.arcsinh(np.abs(np.fft.fftshift(np.fft.fft2(img))))
|
192
|
-
|
193
|
-
diff = _fourier_transform(img1) - _fourier_transform(img2)
|
194
|
-
diff *= gaussian_apodization_window(img1.shape, fwhm_ratio=fwhm_ratio)
|
195
|
-
res = np.abs(diff).max()
|
196
|
-
if return_upper_bound:
|
197
|
-
data_range = np.max(np.abs(img1))
|
198
|
-
return res, np.arcsinh(np.prod(img1.shape) * data_range)
|
199
|
-
else:
|
200
|
-
return res
|
201
|
-
|
202
|
-
|
203
|
-
class SimpleHDF5TomoScanMock:
|
204
|
-
def __init__(self, image_key):
|
205
|
-
self._image_key = image_key
|
206
|
-
|
207
|
-
@property
|
208
|
-
def image_key(self):
|
209
|
-
return self._image_key
|
210
|
-
|
211
|
-
@image_key.setter
|
212
|
-
def image_key(self, image_key):
|
213
|
-
self._image_key = image_key
|
214
|
-
|
215
|
-
def save_reduced_flats(self, *args, **kwargs):
|
216
|
-
pass
|
217
|
-
|
218
|
-
def save_reduced_darks(self, *args, **kwargs):
|
219
|
-
pass
|
220
|
-
|
221
|
-
|
222
|
-
class NXDatasetMock:
|
223
|
-
"""
|
224
|
-
An alternative to tomoscan.esrf.mock.MockHDF5, with a different interface.
|
225
|
-
Attributes are not supported !
|
226
|
-
"""
|
227
|
-
|
228
|
-
def __init__(self, data_volume, image_keys, rotation_angles=None, incident_energy=19.0, other_params=None):
|
229
|
-
self.data_volume = data_volume
|
230
|
-
self.n_proj = data_volume.shape[0]
|
231
|
-
self.image_key = image_keys
|
232
|
-
if rotation_angles is None:
|
233
|
-
rotation_angles = np.linspace(0, 180, self.n_proj, False)
|
234
|
-
self.rotation_angle = rotation_angles
|
235
|
-
self.incident_energy = incident_energy
|
236
|
-
assert image_keys.size == self.n_proj
|
237
|
-
self._finalize_init(other_params)
|
238
|
-
self.dataset_dict = None
|
239
|
-
self.fname = None
|
240
|
-
# Mocks more attributes
|
241
|
-
self.dataset_scanner = SimpleHDF5TomoScanMock(image_key=self.image_key)
|
242
|
-
self.kind = "hdf5"
|
243
|
-
|
244
|
-
def _finalize_init(self, other_params):
|
245
|
-
if other_params is None:
|
246
|
-
other_params = {}
|
247
|
-
default_params = {
|
248
|
-
"detector": {
|
249
|
-
"count_time": 0.05 * np.ones(self.n_proj, dtype="f"),
|
250
|
-
"distance": 0.5,
|
251
|
-
"field_of_view": "Full",
|
252
|
-
"image_key_control": np.copy(self.image_key),
|
253
|
-
"x_pixel_size": 6.5e-6,
|
254
|
-
"y_pixel_size": 6.5e-6,
|
255
|
-
"x_magnified_pixel_size": 6.5e-5,
|
256
|
-
"y_magnified_pixel_size": 6.5e-5,
|
257
|
-
},
|
258
|
-
"sample": {
|
259
|
-
"name": "dummy sample",
|
260
|
-
"x_translation": 5e-4 * np.ones(self.n_proj, dtype="f"),
|
261
|
-
"y_translation": 5e-4 * np.ones(self.n_proj, dtype="f"),
|
262
|
-
"z_translation": 5e-4 * np.ones(self.n_proj, dtype="f"),
|
263
|
-
},
|
264
|
-
}
|
265
|
-
default_params.update(other_params)
|
266
|
-
self.other_params = default_params
|
267
|
-
|
268
|
-
def generate_dict(self):
|
269
|
-
beam_group = {
|
270
|
-
"incident_energy": self.incident_energy,
|
271
|
-
}
|
272
|
-
detector_other_params = self.other_params["detector"]
|
273
|
-
detector_group = {
|
274
|
-
"count_time": detector_other_params["count_time"],
|
275
|
-
"data": self.data_volume,
|
276
|
-
"distance": detector_other_params["distance"],
|
277
|
-
"field_of_view": detector_other_params["field_of_view"],
|
278
|
-
"image_key": self.image_key,
|
279
|
-
"image_key_control": detector_other_params["image_key_control"],
|
280
|
-
"x_pixel_size": detector_other_params["x_pixel_size"],
|
281
|
-
"y_pixel_size": detector_other_params["y_pixel_size"],
|
282
|
-
"x_magnified_pixel_size": detector_other_params["x_magnified_pixel_size"],
|
283
|
-
"y_magnified_pixel_size": detector_other_params["y_magnified_pixel_size"],
|
284
|
-
}
|
285
|
-
sample_other_params = self.other_params["sample"]
|
286
|
-
sample_group = {
|
287
|
-
"name": sample_other_params["name"],
|
288
|
-
"rotation_angle": self.rotation_angle,
|
289
|
-
"x_translation": sample_other_params["x_translation"],
|
290
|
-
"y_translation": sample_other_params["y_translation"],
|
291
|
-
"z_translation": sample_other_params["z_translation"],
|
292
|
-
}
|
293
|
-
self.dataset_dict = {
|
294
|
-
"beam": beam_group,
|
295
|
-
"instrument": {
|
296
|
-
"detector": detector_group,
|
297
|
-
},
|
298
|
-
"sample": sample_group,
|
299
|
-
}
|
300
|
-
|
301
|
-
def generate_hdf5_file(self, fname, h5path=None):
|
302
|
-
self.fname = fname
|
303
|
-
h5path = h5path or "/entry"
|
304
|
-
if self.dataset_dict is None:
|
305
|
-
self.generate_dict()
|
306
|
-
dicttoh5(self.dataset_dict, fname, h5path=h5path, mode="a")
|
307
|
-
# Patch the "data" field which is exported as string by dicttoh5 (?!)
|
308
|
-
self.dataset_path = os.path.join(h5path, "instrument/detector/data")
|
309
|
-
with HDF5File(fname, "a") as fid:
|
310
|
-
del fid[self.dataset_path]
|
311
|
-
fid[self.dataset_path] = self.dataset_dict["instrument"]["detector"]["data"]
|
312
|
-
|
313
|
-
# Mock some of the HDF5DatasetAnalyzer attributes
|
314
|
-
@property
|
315
|
-
def dataset_hdf5_url(self):
|
316
|
-
if self.fname is None:
|
317
|
-
raise ValueError("generate_hdf5_file() was not called")
|
318
|
-
return DataUrl(file_path=self.fname, data_path=self.dataset_path, scheme="silx")
|
319
|
-
|
320
|
-
def _get_images_with_key(self, key):
|
321
|
-
indices = np.arange(self.image_key.size)[self.image_key == key]
|
322
|
-
urls = [
|
323
|
-
DataUrl(
|
324
|
-
file_path=self.fname,
|
325
|
-
data_path=self.dataset_path,
|
326
|
-
data_slice=slice(img_idx, img_idx + 1),
|
327
|
-
scheme="silx",
|
328
|
-
)
|
329
|
-
for img_idx in indices
|
330
|
-
]
|
331
|
-
return dict(zip(indices, urls))
|
332
|
-
|
333
|
-
@property
|
334
|
-
def flats(self):
|
335
|
-
return self._get_images_with_key(1)
|
336
|
-
|
337
|
-
@property
|
338
|
-
def darks(self):
|
339
|
-
return self._get_images_with_key(2)
|
340
|
-
|
341
|
-
def get_data_slices(self, what):
|
342
|
-
images = getattr(self, what)
|
343
|
-
# we can't directly use set() on slice() object (unhashable). Use tuples
|
344
|
-
tuples_list = list(
|
345
|
-
set((du.data_slice().start, du.data_slice().stop) for du in get_compacted_dataslices(images).values())
|
346
|
-
)
|
347
|
-
slices_list = [slice(item[0], item[1]) for item in tuples_list]
|
348
|
-
return slices_list
|
349
|
-
|
350
|
-
|
351
|
-
# To be improved
|
352
|
-
def generate_nx_dataset(out_fname, image_key, data_volume=None, rotation_angle=None):
|
353
|
-
nx_template_file = get_file("dummy.nx.tar.gz")
|
354
|
-
nx_dict = nxtodict(nx_template_file)
|
355
|
-
nx_entry = nx_dict["entry"]
|
356
|
-
|
357
|
-
def _get_field(dict_, path):
|
358
|
-
if path.startswith("/"):
|
359
|
-
path = path[1:]
|
360
|
-
if path.endswith("/"):
|
361
|
-
path = path[:-1]
|
362
|
-
split_path = path.split("/")
|
363
|
-
if len(split_path) == 1:
|
364
|
-
return dict_[split_path[0]]
|
365
|
-
return _get_field(dict_[split_path[0]], "/".join(split_path[1:]))
|
366
|
-
|
367
|
-
for name in ["image_key", "image_key_control"]:
|
368
|
-
nx_entry["data"][name] = image_key
|
369
|
-
nx_entry["instrument"]["detector"][name] = image_key
|
370
|
-
|
371
|
-
if rotation_angle is not None:
|
372
|
-
nx_entry["data"]["rotation_angle"] = rotation_angle
|
373
|
-
nx_entry["sample"]["rotation_angle"] = rotation_angle
|
374
|
-
|
375
|
-
dicttonx(nx_dict, out_fname)
|
File without changes
|