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/resources/nxflatfield.py +0 -217
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- build/lib/nabu/stitching/definitions.py +0 -6
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- build/lib/nabu/stitching/overlap.py +0 -373
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- build/lib/nabu/stitching/z_stitching.py +0 -2279
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- 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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return ZFrameComposition(
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global_end_y=tuple(global_end_ys),
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97
|
-
)
|
98
|
-
|
99
|
-
@staticmethod
|
100
|
-
def compute_stitch_frame_composition(frames, key_lines: tuple, overlap_kernels: tuple, stitching_axis: int):
|
101
|
-
"""
|
102
|
-
compute frame composition for stiching.
|
103
|
-
"""
|
104
|
-
assert len(frames) == len(overlap_kernels) + 1 == len(key_lines) + 1
|
105
|
-
assert stitching_axis in (0, 1, 2)
|
106
|
-
|
107
|
-
# position in the stitched frame;
|
108
|
-
local_start_ys = [0] * len(overlap_kernels)
|
109
|
-
local_end_ys = [kernel.overlap_size for kernel in overlap_kernels]
|
110
|
-
|
111
|
-
# position in the global frame. For this one it is simpler to rely on the raw frame composition
|
112
|
-
composition_raw = ZFrameComposition.compute_raw_frame_compositions(
|
113
|
-
frames=frames,
|
114
|
-
key_lines=key_lines,
|
115
|
-
overlap_kernels=overlap_kernels,
|
116
|
-
stitching_axis=stitching_axis,
|
117
|
-
)
|
118
|
-
global_start_ys = composition_raw.global_end_y[:-1]
|
119
|
-
global_end_ys = composition_raw.global_start_y[1:]
|
120
|
-
|
121
|
-
return ZFrameComposition(
|
122
|
-
local_start_y=tuple(local_start_ys),
|
123
|
-
local_end_y=tuple(local_end_ys),
|
124
|
-
global_start_y=tuple(global_start_ys),
|
125
|
-
global_end_y=tuple(global_end_ys),
|
126
|
-
)
|
127
|
-
|
128
|
-
@staticmethod
|
129
|
-
def pprint_z_stitching(raw_composition, stitch_composition):
|
130
|
-
"""
|
131
|
-
util to display what the output of the z stitch will looks like from composition
|
132
|
-
"""
|
133
|
-
for i_frame, (raw_comp, stitch_comp) in enumerate(zip(raw_composition.browse(), stitch_composition.browse())):
|
134
|
-
raw_local_start, raw_local_end, raw_global_start, raw_global_end = raw_comp
|
135
|
-
|
136
|
-
print(
|
137
|
-
f"stitch_frame[{raw_global_start}:{raw_global_end}] = frame_{i_frame}[{raw_local_start}:{raw_local_end}]"
|
138
|
-
)
|
139
|
-
|
140
|
-
(
|
141
|
-
stitch_local_start,
|
142
|
-
stitch_local_end,
|
143
|
-
stitch_global_start,
|
144
|
-
stitch_global_end,
|
145
|
-
) = stitch_comp
|
146
|
-
|
147
|
-
print(
|
148
|
-
f"stitch_frame[{stitch_global_start}:{stitch_global_end}] = stitched_frame_{i_frame}[{stitch_local_start}:{stitch_local_end}]"
|
149
|
-
)
|
150
|
-
else:
|
151
|
-
i_frame += 1
|
152
|
-
raw_local_start, raw_local_end, raw_global_start, raw_global_end = list(raw_composition.browse())[-1]
|
153
|
-
print(
|
154
|
-
f"stitch_frame[{raw_global_start}:{raw_global_end}] = frame_{i_frame}[{raw_local_start}:{raw_local_end}]"
|
155
|
-
)
|
build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/overlap.py
DELETED
@@ -1,373 +0,0 @@
|
|
1
|
-
# coding: utf-8
|
2
|
-
# /*##########################################################################
|
3
|
-
#
|
4
|
-
# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
|
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|
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#
|
6
|
-
# Permission is hereby granted, free of charge, to any person obtaining a copy
|
7
|
-
# of this software and associated documentation files (the "Software"), to deal
|
8
|
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# in the Software without restriction, including without limitation the rights
|
9
|
-
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
|
10
|
-
# copies of the Software, and to permit persons to whom the Software is
|
11
|
-
# furnished to do so, subject to the following conditions:
|
12
|
-
#
|
13
|
-
# The above copyright notice and this permission notice shall be included in
|
14
|
-
# all copies or substantial portions of the Software.
|
15
|
-
#
|
16
|
-
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
|
17
|
-
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
|
18
|
-
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
|
19
|
-
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
|
20
|
-
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
|
21
|
-
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
|
22
|
-
# THE SOFTWARE.
|
23
|
-
#
|
24
|
-
# ###########################################################################*/
|
25
|
-
|
26
|
-
__authors__ = ["H. Payno"]
|
27
|
-
__license__ = "MIT"
|
28
|
-
__date__ = "10/05/2022"
|
29
|
-
|
30
|
-
|
31
|
-
import numpy
|
32
|
-
import logging
|
33
|
-
from typing import Optional, Union
|
34
|
-
from silx.utils.enum import Enum as _Enum
|
35
|
-
from nabu.misc import fourier_filters
|
36
|
-
from scipy.fft import rfftn as local_fftn
|
37
|
-
from scipy.fft import irfftn as local_ifftn
|
38
|
-
from tomoscan.utils.geometry import BoundingBox1D
|
39
|
-
|
40
|
-
_logger = logging.getLogger(__name__)
|
41
|
-
|
42
|
-
|
43
|
-
class OverlapStitchingStrategy(_Enum):
|
44
|
-
MEAN = "mean"
|
45
|
-
COSINUS_WEIGHTS = "cosinus weights"
|
46
|
-
LINEAR_WEIGHTS = "linear weights"
|
47
|
-
CLOSEST = "closest"
|
48
|
-
IMAGE_MINIMUM_DIVERGENCE = "image minimum divergence"
|
49
|
-
HIGHER_SIGNAL = "higher signal"
|
50
|
-
|
51
|
-
|
52
|
-
DEFAULT_OVERLAP_STRATEGY = OverlapStitchingStrategy.COSINUS_WEIGHTS
|
53
|
-
|
54
|
-
DEFAULT_OVERLAP_SIZE = None # could also be an int
|
55
|
-
# default overlap to be take for stitching. Ig None: take the largest possible area
|
56
|
-
|
57
|
-
|
58
|
-
class OverlapKernelBase:
|
59
|
-
pass
|
60
|
-
|
61
|
-
|
62
|
-
class ZStichOverlapKernel(OverlapKernelBase):
|
63
|
-
"""
|
64
|
-
class used to define overlap between two scans and create stitch between frames (`stitch` function)
|
65
|
-
"""
|
66
|
-
|
67
|
-
DEFAULT_HIGH_FREQUENCY_THRESHOLD = 2
|
68
|
-
|
69
|
-
def __init__(
|
70
|
-
self,
|
71
|
-
frame_width: int,
|
72
|
-
stitching_strategy: OverlapStitchingStrategy = DEFAULT_OVERLAP_STRATEGY,
|
73
|
-
overlap_size: int = DEFAULT_OVERLAP_SIZE,
|
74
|
-
extra_params: Optional[dict] = None,
|
75
|
-
) -> None:
|
76
|
-
""" """
|
77
|
-
from nabu.stitching.config import KEY_THRESHOLD_FREQUENCY # avoid acylic import
|
78
|
-
|
79
|
-
if not isinstance(overlap_size, int) and overlap_size > 0:
|
80
|
-
raise TypeError(
|
81
|
-
f"overlap_size is expected to be a positive int, {overlap_size} - not {overlap_size} ({type(overlap_size)})"
|
82
|
-
)
|
83
|
-
if not isinstance(frame_width, int) or not frame_width > 0:
|
84
|
-
raise TypeError(
|
85
|
-
f"frame_width is expected to be a positive int, {frame_width} - not {frame_width} ({type(frame_width)})"
|
86
|
-
)
|
87
|
-
|
88
|
-
self._overlap_size = abs(overlap_size)
|
89
|
-
self._frame_width = frame_width
|
90
|
-
self._stitching_strategy = OverlapStitchingStrategy.from_value(stitching_strategy)
|
91
|
-
self._weights_img_1 = None
|
92
|
-
self._weights_img_2 = None
|
93
|
-
if extra_params is None:
|
94
|
-
extra_params = {}
|
95
|
-
self._high_frequency_threshold = extra_params.get(
|
96
|
-
KEY_THRESHOLD_FREQUENCY, self.DEFAULT_HIGH_FREQUENCY_THRESHOLD
|
97
|
-
)
|
98
|
-
|
99
|
-
def __str__(self) -> str:
|
100
|
-
return f"z-stitching kernel (policy={self.stitching_strategy.value}, overlap_size={self.overlap_size}, frame={self._frame_width})"
|
101
|
-
|
102
|
-
@staticmethod
|
103
|
-
def __check_img(img, name):
|
104
|
-
if not isinstance(img, numpy.ndarray) and img.ndim == 2:
|
105
|
-
raise ValueError(f"{name} is expected to be 2D numpy array")
|
106
|
-
|
107
|
-
@property
|
108
|
-
def overlap_size(self) -> int:
|
109
|
-
return self._overlap_size
|
110
|
-
|
111
|
-
@overlap_size.setter
|
112
|
-
def overlap_size(self, size: int):
|
113
|
-
if not isinstance(size, int):
|
114
|
-
raise TypeError(f"height expects a int ({type(size)} provided instead)")
|
115
|
-
if not size >= 0:
|
116
|
-
raise ValueError(f"height is expected to be positive")
|
117
|
-
self._overlap_size = abs(size)
|
118
|
-
# update weights if needed
|
119
|
-
if self._weights_img_1 is not None or self._weights_img_2 is not None:
|
120
|
-
self.compute_weights()
|
121
|
-
|
122
|
-
@property
|
123
|
-
def img_2(self) -> numpy.ndarray:
|
124
|
-
return self._img_2
|
125
|
-
|
126
|
-
@property
|
127
|
-
def weights_img_1(self) -> Optional[numpy.ndarray]:
|
128
|
-
return self._weights_img_1
|
129
|
-
|
130
|
-
@property
|
131
|
-
def weights_img_2(self) -> Optional[numpy.ndarray]:
|
132
|
-
return self._weights_img_2
|
133
|
-
|
134
|
-
@property
|
135
|
-
def stitching_strategy(self) -> OverlapStitchingStrategy:
|
136
|
-
return self._stitching_strategy
|
137
|
-
|
138
|
-
def compute_weights(self):
|
139
|
-
if self.stitching_strategy is OverlapStitchingStrategy.MEAN:
|
140
|
-
weights_img_1 = numpy.ones(self._overlap_size) * 0.5
|
141
|
-
weights_img_2 = weights_img_1[::-1]
|
142
|
-
elif self.stitching_strategy is OverlapStitchingStrategy.CLOSEST:
|
143
|
-
n_item = self._overlap_size // 2 + self._overlap_size % 2
|
144
|
-
weights_img_1 = numpy.concatenate(
|
145
|
-
[
|
146
|
-
numpy.ones(n_item),
|
147
|
-
numpy.zeros(self._overlap_size - n_item),
|
148
|
-
]
|
149
|
-
)
|
150
|
-
weights_img_2 = numpy.concatenate(
|
151
|
-
[
|
152
|
-
numpy.zeros(n_item),
|
153
|
-
numpy.ones(self._overlap_size - n_item),
|
154
|
-
]
|
155
|
-
)
|
156
|
-
elif self.stitching_strategy is OverlapStitchingStrategy.LINEAR_WEIGHTS:
|
157
|
-
weights_img_1 = numpy.linspace(1.0, 0.0, self._overlap_size)
|
158
|
-
weights_img_2 = weights_img_1[::-1]
|
159
|
-
elif self.stitching_strategy is OverlapStitchingStrategy.COSINUS_WEIGHTS:
|
160
|
-
angles = numpy.linspace(0.0, numpy.pi / 2.0, self._overlap_size)
|
161
|
-
weights_img_1 = numpy.cos(angles) ** 2
|
162
|
-
weights_img_2 = numpy.sin(angles) ** 2
|
163
|
-
elif self.stitching_strategy in (
|
164
|
-
OverlapStitchingStrategy.IMAGE_MINIMUM_DIVERGENCE,
|
165
|
-
OverlapStitchingStrategy.HIGHER_SIGNAL,
|
166
|
-
):
|
167
|
-
# those strategies are not using constant weights but have treatments depending on the provided img_1 and mg_2 during stitching
|
168
|
-
return
|
169
|
-
else:
|
170
|
-
raise NotImplementedError(f"{self.stitching_strategy} not implemented")
|
171
|
-
|
172
|
-
self._weights_img_1 = weights_img_1.reshape(-1, 1) * numpy.ones(self._frame_width).reshape(1, -1)
|
173
|
-
self._weights_img_2 = weights_img_2.reshape(-1, 1) * numpy.ones(self._frame_width).reshape(1, -1)
|
174
|
-
|
175
|
-
def stitch(self, img_1, img_2, check_input=True) -> tuple:
|
176
|
-
"""Compute overlap region from the defined strategy"""
|
177
|
-
if check_input:
|
178
|
-
self.__check_img(img_1, "img_1")
|
179
|
-
self.__check_img(img_2, "img_2")
|
180
|
-
|
181
|
-
if img_1.shape != img_2.shape:
|
182
|
-
raise ValueError(
|
183
|
-
f"both images are expected to be of the same shape to apply stitch ({img_1.shape} vs {img_2.shape})"
|
184
|
-
)
|
185
|
-
|
186
|
-
if self._stitching_strategy is OverlapStitchingStrategy.IMAGE_MINIMUM_DIVERGENCE:
|
187
|
-
return (
|
188
|
-
compute_image_minimum_divergence(
|
189
|
-
img_1=img_1, img_2=img_2, high_frequency_threshold=self._high_frequency_threshold
|
190
|
-
),
|
191
|
-
None,
|
192
|
-
None,
|
193
|
-
)
|
194
|
-
elif self._stitching_strategy is OverlapStitchingStrategy.HIGHER_SIGNAL:
|
195
|
-
return (
|
196
|
-
compute_image_higher_signal(img_1=img_1, img_2=img_2),
|
197
|
-
None,
|
198
|
-
None,
|
199
|
-
)
|
200
|
-
else:
|
201
|
-
if self.weights_img_1 is None or self.weights_img_2 is None:
|
202
|
-
self.compute_weights()
|
203
|
-
|
204
|
-
return (
|
205
|
-
img_1 * self.weights_img_1 + img_2 * self.weights_img_2,
|
206
|
-
self.weights_img_1,
|
207
|
-
self.weights_img_2,
|
208
|
-
)
|
209
|
-
|
210
|
-
|
211
|
-
def compute_image_minimum_divergence(img_1: numpy.ndarray, img_2: numpy.ndarray, high_frequency_threshold):
|
212
|
-
"""
|
213
|
-
Algorithm to improve treatment of high frequency.
|
214
|
-
|
215
|
-
It split the two images into two parts: high frequency and low frequency.
|
216
|
-
|
217
|
-
The two low frequency part will be stitched using a 'sinusoidal' / cosinus weights approach.
|
218
|
-
When the two high frequency parts will be stitched by taking the lower divergent pixels
|
219
|
-
"""
|
220
|
-
|
221
|
-
# split low and high frequencies
|
222
|
-
def split_image(image: numpy.ndarray, threshold: int) -> tuple:
|
223
|
-
"""split an image to return (low_frequency, high_frequency)"""
|
224
|
-
|
225
|
-
lowpass_filter = fourier_filters.get_lowpass_filter(
|
226
|
-
image.shape[-2:],
|
227
|
-
cutoff_par=threshold,
|
228
|
-
use_rfft=True,
|
229
|
-
data_type=image.dtype,
|
230
|
-
)
|
231
|
-
highpass_filter = fourier_filters.get_highpass_filter(
|
232
|
-
image.shape[-2:],
|
233
|
-
cutoff_par=threshold,
|
234
|
-
use_rfft=True,
|
235
|
-
data_type=image.dtype,
|
236
|
-
)
|
237
|
-
low_fre_part = local_ifftn(local_fftn(image, axes=(-2, -1)) * lowpass_filter, axes=(-2, -1)).real
|
238
|
-
high_fre_part = local_ifftn(local_fftn(image, axes=(-2, -1)) * highpass_filter, axes=(-2, -1)).real
|
239
|
-
return (low_fre_part, high_fre_part)
|
240
|
-
|
241
|
-
low_freq_img_1, high_freq_img_1 = split_image(img_1, threshold=high_frequency_threshold)
|
242
|
-
low_freq_img_2, high_freq_img_2 = split_image(img_2, threshold=high_frequency_threshold)
|
243
|
-
|
244
|
-
# handle low frequency
|
245
|
-
low_freq_stitching_kernel = ZStichOverlapKernel(
|
246
|
-
frame_width=img_1.shape[1],
|
247
|
-
stitching_strategy=OverlapStitchingStrategy.COSINUS_WEIGHTS,
|
248
|
-
overlap_size=img_1.shape[0],
|
249
|
-
)
|
250
|
-
low_freq_stitched = low_freq_stitching_kernel.stitch(
|
251
|
-
img_1=low_freq_img_1,
|
252
|
-
img_2=low_freq_img_2,
|
253
|
-
check_input=False,
|
254
|
-
)[0]
|
255
|
-
|
256
|
-
# handle high frequency
|
257
|
-
mean_high_frequency = numpy.mean([high_freq_img_1, high_freq_img_2])
|
258
|
-
assert numpy.isscalar(mean_high_frequency)
|
259
|
-
high_freq_distance_img_1 = numpy.abs(high_freq_img_1 - mean_high_frequency)
|
260
|
-
high_freq_distance_img_2 = numpy.abs(high_freq_img_2 - mean_high_frequency)
|
261
|
-
high_freq_stitched = numpy.where(
|
262
|
-
high_freq_distance_img_1 >= high_freq_distance_img_2, high_freq_distance_img_2, high_freq_distance_img_1
|
263
|
-
)
|
264
|
-
|
265
|
-
# merge back low and high frequencies together
|
266
|
-
def merge_images(low_freq: numpy.ndarray, high_freq: numpy.ndarray) -> numpy.ndarray:
|
267
|
-
"""merge two part of an image. The low frequency part with the high frequency part"""
|
268
|
-
return low_freq + high_freq
|
269
|
-
|
270
|
-
return merge_images(low_freq_stitched, high_freq_stitched)
|
271
|
-
|
272
|
-
|
273
|
-
def compute_image_higher_signal(img_1: numpy.ndarray, img_2: numpy.ndarray):
|
274
|
-
"""
|
275
|
-
the higher signal will pick pixel on the image having the higher signal.
|
276
|
-
A use case is that if there is some artefacts on images which creates stripes (from scintillator artefacts for example)
|
277
|
-
it could be removed from this method
|
278
|
-
"""
|
279
|
-
# note: to be think about. But maybe it can be interesting to rescale img_1 and img_2
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# to ge something more coherent
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return numpy.where(img_1 >= img_2, img_1, img_2)
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def check_overlaps(frames: Union[tuple, numpy.ndarray], positions: tuple, axis: int, raise_error: bool):
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"""
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check over frames if there is a single overlap other juxtaposed frames (at most and at least)
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:param frames: liste of ordered / sorted frames along axis to test (from higher to lower)
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:param positions: positions of frames in 3D space as (position axis 0, position axis 1, position axis 2)
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:param axis: axis to check
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:param raise_error: if True then raise an error if two frames don't have at least and at most one overlap. Else log an error
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"""
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if not isinstance(frames, (tuple, numpy.ndarray)):
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raise TypeError(f"frames is expected to be a tuple or a numpy array. Get {type(frames)} instead")
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if not isinstance(positions, tuple):
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raise TypeError(f"positions is expected to be a tuple. Get {type(positions)} instead")
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assert isinstance(axis, int), "axis is expected to be an int"
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assert isinstance(raise_error, bool), "raise_error is expected to be a bool"
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def treat_error(error_msg: str):
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if raise_error:
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raise ValueError(error_msg)
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else:
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_logger.error(raise_error)
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# convert each frame to appropriate bounding box according to the axis
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def convert_to_bb(frame: numpy.ndarray, position: tuple, axis: int):
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assert isinstance(axis, int)
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assert isinstance(position, tuple), f"position expected a tuple. Get {type(position)} instead"
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310
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start_frame = position[axis] - frame.shape[axis] // 2
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end_frame = start_frame + frame.shape[axis]
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return BoundingBox1D(start_frame, end_frame)
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314
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bounding_boxes = {
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315
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convert_to_bb(frame=frame, position=position, axis=axis): position for frame, position in zip(frames, positions)
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}
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317
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318
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def get_frame_index(my_bb) -> str:
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319
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bb_index = tuple(bounding_boxes.keys()).index(my_bb) + 1
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320
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if bb_index in (1, 21, 31):
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321
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return f"{bb_index}st"
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322
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elif bb_index in (2, 22, 32):
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323
|
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return f"{bb_index}nd"
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324
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elif bb_index == (3, 23, 33):
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325
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return f"{bb_index}rd"
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326
|
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else:
|
327
|
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return f"{bb_index}th"
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328
|
-
|
329
|
-
# check that theres an overlap between two juxtaposed bb (or frame at the end)
|
330
|
-
all_bounding_boxes = tuple(bounding_boxes.keys())
|
331
|
-
bb_with_expected_overlap = [
|
332
|
-
(bb_frame, bb_next_frame) for bb_frame, bb_next_frame in zip(all_bounding_boxes[:-1], all_bounding_boxes[1:])
|
333
|
-
]
|
334
|
-
|
335
|
-
for bb_pair in bb_with_expected_overlap:
|
336
|
-
bb_frame, bb_next_frame = bb_pair
|
337
|
-
if bb_frame.max < bb_next_frame.min:
|
338
|
-
treat_error(f"provided frames seems un sorted (from the higher to the lower)")
|
339
|
-
if bb_frame.min < bb_next_frame.min:
|
340
|
-
treat_error(
|
341
|
-
f"Seems like {get_frame_index(bb_frame)} frame is fully overlaping with frame {get_frame_index(bb_next_frame)}"
|
342
|
-
)
|
343
|
-
if bb_frame.get_overlap(bb_next_frame) is None:
|
344
|
-
treat_error(
|
345
|
-
f"no overlap found between two juxtaposed frames - {get_frame_index(bb_frame)} and {get_frame_index(bb_next_frame)}"
|
346
|
-
)
|
347
|
-
|
348
|
-
# check there is no overlap between none juxtaposed bb
|
349
|
-
def pick_all_none_juxtaposed_bb(index, my_bounding_boxes: tuple):
|
350
|
-
"""return all the bounding boxes to check for the index 'index':
|
351
|
-
|
352
|
-
:return: (tested_bounding_box, bounding_boxes_to_test)
|
353
|
-
"""
|
354
|
-
my_bounding_boxes = {bb_index: bb for bb_index, bb in enumerate(my_bounding_boxes)}
|
355
|
-
bounding_boxes = dict(
|
356
|
-
filter(
|
357
|
-
lambda pair: pair[0] not in (index - 1, index, index + 1),
|
358
|
-
my_bounding_boxes.items(),
|
359
|
-
)
|
360
|
-
)
|
361
|
-
return my_bounding_boxes[index], bounding_boxes.values()
|
362
|
-
|
363
|
-
bb_without_expected_overlap = [
|
364
|
-
pick_all_none_juxtaposed_bb(index, all_bounding_boxes) for index in range(len(all_bounding_boxes))
|
365
|
-
]
|
366
|
-
|
367
|
-
for bb_pair in bb_without_expected_overlap:
|
368
|
-
bb_frame, bb_not_juxtaposed_frames = bb_pair
|
369
|
-
for bb_not_juxtaposed_frame in bb_not_juxtaposed_frames:
|
370
|
-
if bb_frame.get_overlap(bb_not_juxtaposed_frame) is not None:
|
371
|
-
treat_error(
|
372
|
-
f"overlap found between two frames not juxtaposed - {bounding_boxes[bb_frame]} and {bounding_boxes[bb_not_juxtaposed_frame]}"
|
373
|
-
)
|
@@ -1,60 +0,0 @@
|
|
1
|
-
import numpy
|
2
|
-
from silx.utils.enum import Enum as _Enum
|
3
|
-
|
4
|
-
|
5
|
-
class SampleSide(_Enum):
|
6
|
-
LEFT = "left"
|
7
|
-
RIGHT = "right"
|
8
|
-
|
9
|
-
|
10
|
-
class Method(_Enum):
|
11
|
-
MEAN = "mean"
|
12
|
-
MEDIAN = "median"
|
13
|
-
|
14
|
-
|
15
|
-
def normalize_frame(
|
16
|
-
frame: numpy.ndarray, side: SampleSide, method: Method, sample_width: int = 50, margin_before_sample: int = 0
|
17
|
-
):
|
18
|
-
"""
|
19
|
-
normalize the frame from a sample section picked at the left of the right of the frame
|
20
|
-
|
21
|
-
:param frame: frame to normalize
|
22
|
-
:param SampleSide side: side to pick the sample
|
23
|
-
:param Method method: normalization method
|
24
|
-
:param int sample_width: sample width
|
25
|
-
:param int margin: margin before the sampling area
|
26
|
-
"""
|
27
|
-
if not isinstance(frame, numpy.ndarray):
|
28
|
-
raise TypeError(f"Frame is expected to be a 2D numpy array.")
|
29
|
-
if frame.ndim != 2:
|
30
|
-
raise TypeError(f"Frame is expected to be a 2D numpy array. Get {frame.ndim}D")
|
31
|
-
side = SampleSide.from_value(side)
|
32
|
-
method = Method.from_value(method)
|
33
|
-
|
34
|
-
if frame.shape[1] < sample_width + margin_before_sample:
|
35
|
-
raise ValueError(
|
36
|
-
f"frame width ({frame.shape[1]}) < sample_width + margin ({sample_width + margin_before_sample})"
|
37
|
-
)
|
38
|
-
|
39
|
-
# create sample
|
40
|
-
if side is SampleSide.LEFT:
|
41
|
-
sample_start = margin_before_sample
|
42
|
-
sample_end = margin_before_sample + sample_width
|
43
|
-
sample = frame[:, sample_start:sample_end]
|
44
|
-
elif side is SampleSide.RIGHT:
|
45
|
-
sample_start = frame.shape[1] - (sample_width + margin_before_sample)
|
46
|
-
sample_end = frame.shape[1] - margin_before_sample
|
47
|
-
sample = frame[:, sample_start:sample_end]
|
48
|
-
else:
|
49
|
-
raise ValueError(f"side {side.value} not handled")
|
50
|
-
|
51
|
-
# do normalization
|
52
|
-
if method is Method.MEAN:
|
53
|
-
normalization_array = numpy.mean(sample, axis=1)
|
54
|
-
elif method is Method.MEDIAN:
|
55
|
-
normalization_array = numpy.median(sample, axis=1)
|
56
|
-
else:
|
57
|
-
raise ValueError(f"side {side.value} not handled")
|
58
|
-
for line in range(normalization_array.shape[0]):
|
59
|
-
frame[line, :] -= normalization_array[line]
|
60
|
-
return frame
|