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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from distutils.version import StrictVersion
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import logging
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from nxtomo.utils.transformation import build_matrix, UDDetTransformation
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from nxtomo.utils.transformation import build_matrix, UDDetTransformation
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from .overlap import OverlapStitchingStrategy, ZStichOverlapKernel
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from .alignment import AlignmentAxis1, AlignmentAxis2, PaddedRawData
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from ..misc import fourier_filters
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"Unable to load skimage. Please install it if you want to use it for finding shifts from `find_relative_shifts`"
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)
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class ShiftAlgorithm(_Enum):
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# In the case of shift search on radio along axis 2 (or axis x in image space) we can benefit from the existing
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"""
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stitch the two ovrelap with all the requested strategies.
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frame_width=overlap_1.shape[1],
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stiched_overlap, w1, w2 = stitcher.stitch(overlap_1, overlap_2, check_input=True)
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"stitching": stiched_overlap,
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"weights_overlap_2": w2,
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}
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return res
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def find_frame_relative_shifts(
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estimated_shifts,
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x_shifts_params: Optional[dict] = None,
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98
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y_shifts_params: Optional[dict] = None,
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):
|
100
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from nabu.stitching.config import (
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101
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KEY_WINDOW_SIZE,
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102
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KEY_LOW_PASS_FILTER,
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103
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KEY_HIGH_PASS_FILTER,
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104
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) # avoid cyclic import
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105
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-
|
106
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x_cross_correlation_function = ShiftAlgorithm.from_value(x_cross_correlation_function)
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107
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y_cross_correlation_function = ShiftAlgorithm.from_value(y_cross_correlation_function)
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108
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-
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109
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if x_shifts_params is None:
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110
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x_shifts_params = {}
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111
|
-
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112
|
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if y_shifts_params is None:
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113
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y_shifts_params = {}
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114
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-
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115
|
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# apply filtering if any
|
116
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def _str_to_int(value):
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117
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if isinstance(value, str):
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118
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value = value.lstrip("'").lstrip('"')
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119
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value = value.rstrip("'").rstrip('"')
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120
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value = int(value)
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121
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return value
|
122
|
-
|
123
|
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low_pass = _str_to_int(x_shifts_params.get(KEY_LOW_PASS_FILTER, y_shifts_params.get(KEY_LOW_PASS_FILTER, None)))
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124
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high_pass = _str_to_int(x_shifts_params.get(KEY_HIGH_PASS_FILTER, y_shifts_params.get(KEY_HIGH_PASS_FILTER, None)))
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125
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if high_pass is None and low_pass is None:
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126
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pass
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127
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else:
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128
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if low_pass is None:
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129
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low_pass = 1
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130
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if high_pass is None:
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131
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high_pass = 20
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_logger.info(f"filter image for shift search (low_pass={low_pass}, high_pass={high_pass})")
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133
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img_filter = fourier_filters.get_bandpass_filter(
|
134
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overlap_upper_frame.shape[-2:],
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135
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cutoff_lowpass=low_pass,
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136
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cutoff_highpass=high_pass,
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137
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use_rfft=True,
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138
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data_type=overlap_upper_frame.dtype,
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139
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)
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140
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overlap_upper_frame = local_ifftn(
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141
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local_fftn(overlap_upper_frame, axes=(-2, -1)) * img_filter, axes=(-2, -1)
|
142
|
-
).real
|
143
|
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overlap_lower_frame = local_ifftn(
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144
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-
local_fftn(overlap_lower_frame, axes=(-2, -1)) * img_filter, axes=(-2, -1)
|
145
|
-
).real
|
146
|
-
|
147
|
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# compute shifts
|
148
|
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initial_shifts = numpy.array(estimated_shifts).copy()
|
149
|
-
extra_shifts = numpy.array([0.0, 0.0])
|
150
|
-
|
151
|
-
def skimage_proxy(img1, img2):
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152
|
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if not __has_sk_phase_correlation__:
|
153
|
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raise ValueError("scikit-image not installed. Cannot do phase correlation from it")
|
154
|
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else:
|
155
|
-
found_shift, _, _ = phase_cross_correlation(reference_image=img1, moving_image=img2, space="real")
|
156
|
-
return -found_shift
|
157
|
-
|
158
|
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shift_methods = {
|
159
|
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ShiftAlgorithm.NABU_FFT: functools.partial(
|
160
|
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find_shift_correlate, img1=overlap_upper_frame, img2=overlap_lower_frame
|
161
|
-
),
|
162
|
-
ShiftAlgorithm.SKIMAGE: functools.partial(skimage_proxy, img1=overlap_upper_frame, img2=overlap_lower_frame),
|
163
|
-
ShiftAlgorithm.ITK_IMG_REG_V4: functools.partial(
|
164
|
-
find_shift_with_itk, img1=overlap_upper_frame, img2=overlap_lower_frame
|
165
|
-
),
|
166
|
-
ShiftAlgorithm.NONE: functools.partial(lambda: (0.0, 0.0)),
|
167
|
-
}
|
168
|
-
|
169
|
-
res_algo = {}
|
170
|
-
for shift_alg in set((x_cross_correlation_function, y_cross_correlation_function)):
|
171
|
-
if shift_alg not in shift_methods:
|
172
|
-
raise ValueError(f"requested image alignment function not handled ({shift_alg})")
|
173
|
-
try:
|
174
|
-
res_algo[shift_alg] = shift_methods[shift_alg]()
|
175
|
-
except Exception as e:
|
176
|
-
_logger.error(f"Failed to find shift from {shift_alg.value}. Error is {e}")
|
177
|
-
res_algo[shift_alg] = (0, 0)
|
178
|
-
|
179
|
-
extra_shifts = (
|
180
|
-
res_algo[y_cross_correlation_function][0],
|
181
|
-
res_algo[x_cross_correlation_function][1],
|
182
|
-
)
|
183
|
-
|
184
|
-
final_rel_shifts = numpy.array(extra_shifts) + initial_shifts
|
185
|
-
return tuple([int(shift) for shift in final_rel_shifts])
|
186
|
-
|
187
|
-
|
188
|
-
def find_volumes_relative_shifts(
|
189
|
-
upper_volume: VolumeBase,
|
190
|
-
lower_volume: VolumeBase,
|
191
|
-
estimated_shifts,
|
192
|
-
dim_axis_1: int,
|
193
|
-
dtype,
|
194
|
-
flip_ud_upper_frame: bool = False,
|
195
|
-
flip_ud_lower_frame: bool = False,
|
196
|
-
slice_for_shift: Union[int, str] = "middle",
|
197
|
-
x_cross_correlation_function=None,
|
198
|
-
y_cross_correlation_function=None,
|
199
|
-
x_shifts_params: Optional[dict] = None,
|
200
|
-
y_shifts_params: Optional[dict] = None,
|
201
|
-
alignment_axis_2="center",
|
202
|
-
alignment_axis_1="center",
|
203
|
-
):
|
204
|
-
"""
|
205
|
-
|
206
|
-
:param int dim_axis_1: axis 1 dimension (to handle axis 1 alignment)
|
207
|
-
"""
|
208
|
-
if y_shifts_params is None:
|
209
|
-
y_shifts_params = {}
|
210
|
-
|
211
|
-
if x_shifts_params is None:
|
212
|
-
x_shifts_params = {}
|
213
|
-
|
214
|
-
alignment_axis_2 = AlignmentAxis2.from_value(alignment_axis_2)
|
215
|
-
alignment_axis_1 = AlignmentAxis1.from_value(alignment_axis_1)
|
216
|
-
assert dim_axis_1 > 0, "dim_axis_1 <= 0"
|
217
|
-
|
218
|
-
if isinstance(slice_for_shift, str):
|
219
|
-
if slice_for_shift == "first":
|
220
|
-
slice_for_shift = 0
|
221
|
-
elif slice_for_shift == "last":
|
222
|
-
slice_for_shift = dim_axis_1
|
223
|
-
elif slice_for_shift == "middle":
|
224
|
-
slice_for_shift = dim_axis_1 // 2
|
225
|
-
else:
|
226
|
-
raise ValueError("invalid slice provided to search shift", slice_for_shift)
|
227
|
-
|
228
|
-
def get_slice_along_axis_1(volume: VolumeBase, index: int):
|
229
|
-
assert isinstance(index, int), f"index should be an int, {type(index)} provided"
|
230
|
-
volume_shape = volume.get_volume_shape()
|
231
|
-
if alignment_axis_1 is AlignmentAxis1.BACK:
|
232
|
-
front_empty_width = dim_axis_1 - volume_shape[1]
|
233
|
-
if index < front_empty_width:
|
234
|
-
return PaddedRawData.get_empty_frame(shape=(volume_shape[0], volume_shape[2]), dtype=dtype)
|
235
|
-
else:
|
236
|
-
return volume.get_slice(index=index - front_empty_width, axis=1)
|
237
|
-
elif alignment_axis_1 is AlignmentAxis1.FRONT:
|
238
|
-
if index >= volume_shape[1]:
|
239
|
-
return PaddedRawData.get_empty_frame(shape=(volume_shape[0], volume_shape[2]), dtype=dtype)
|
240
|
-
else:
|
241
|
-
return volume.get_slice(index=index, axis=1)
|
242
|
-
elif alignment_axis_1 is AlignmentAxis1.CENTER:
|
243
|
-
front_empty_width = (dim_axis_1 - volume_shape[1]) // 2
|
244
|
-
back_empty_width = dim_axis_1 - front_empty_width
|
245
|
-
if index < front_empty_width or index > back_empty_width:
|
246
|
-
return PaddedRawData.get_empty_frame(shape=(volume_shape[0], volume_shape[2]), dtype=dtype)
|
247
|
-
else:
|
248
|
-
return volume.get_slice(index=index - front_empty_width, axis=1)
|
249
|
-
else:
|
250
|
-
raise TypeError(f"unmanaged alignment mode {alignment_axis_1.value}")
|
251
|
-
|
252
|
-
upper_frame = get_slice_along_axis_1(upper_volume, index=slice_for_shift)
|
253
|
-
lower_frame = get_slice_along_axis_1(lower_volume, index=slice_for_shift)
|
254
|
-
if flip_ud_upper_frame:
|
255
|
-
upper_frame = numpy.flipud(upper_frame.copy())
|
256
|
-
if flip_ud_lower_frame:
|
257
|
-
lower_frame = numpy.flipud(lower_frame.copy())
|
258
|
-
|
259
|
-
from nabu.stitching.config import KEY_WINDOW_SIZE # avoid cyclic import
|
260
|
-
|
261
|
-
w_window_size = int(y_shifts_params.get(KEY_WINDOW_SIZE, 400))
|
262
|
-
start_overlap = max(estimated_shifts[0] // 2 - w_window_size // 2, 0)
|
263
|
-
end_overlap = min(estimated_shifts[0] // 2 + w_window_size // 2, min(upper_frame.shape[0], lower_frame.shape[0]))
|
264
|
-
|
265
|
-
if start_overlap == 0:
|
266
|
-
overlap_upper_frame = upper_frame[-end_overlap:]
|
267
|
-
else:
|
268
|
-
overlap_upper_frame = upper_frame[-end_overlap:-start_overlap]
|
269
|
-
overlap_lower_frame = lower_frame[start_overlap:end_overlap]
|
270
|
-
|
271
|
-
# align if necessary
|
272
|
-
if overlap_upper_frame.shape[1] != overlap_lower_frame.shape[1]:
|
273
|
-
overlap_frame_width = min(overlap_upper_frame.shape[1], overlap_lower_frame.shape[1])
|
274
|
-
if alignment_axis_2 is AlignmentAxis2.CENTER:
|
275
|
-
upper_frame_left_pos = overlap_upper_frame.shape[1] // 2 - overlap_frame_width // 2
|
276
|
-
upper_frame_right_pos = upper_frame_left_pos + overlap_frame_width
|
277
|
-
overlap_upper_frame = overlap_upper_frame[:, upper_frame_left_pos:upper_frame_right_pos]
|
278
|
-
|
279
|
-
lower_frame_left_pos = overlap_lower_frame.shape[1] // 2 - overlap_frame_width // 2
|
280
|
-
lower_frame_right_pos = lower_frame_left_pos + overlap_frame_width
|
281
|
-
overlap_lower_frame = overlap_lower_frame[:, lower_frame_left_pos:lower_frame_right_pos]
|
282
|
-
elif alignment_axis_2 is AlignmentAxis2.LEFT:
|
283
|
-
overlap_upper_frame = overlap_upper_frame[:, :overlap_frame_width]
|
284
|
-
overlap_lower_frame = overlap_lower_frame[:, :overlap_frame_width]
|
285
|
-
elif alignment_axis_2 is AlignmentAxis2.RIGTH:
|
286
|
-
overlap_upper_frame = overlap_upper_frame[:, -overlap_frame_width:]
|
287
|
-
overlap_lower_frame = overlap_lower_frame[:, -overlap_frame_width:]
|
288
|
-
else:
|
289
|
-
raise ValueError(f"Alignement {alignment_axis_2.value} is not handled")
|
290
|
-
|
291
|
-
if not overlap_upper_frame.shape == overlap_lower_frame.shape:
|
292
|
-
raise ValueError(f"Fail to get consistant overlap ({overlap_upper_frame.shape} vs {overlap_lower_frame.shape})")
|
293
|
-
|
294
|
-
return find_frame_relative_shifts(
|
295
|
-
overlap_upper_frame=overlap_upper_frame,
|
296
|
-
overlap_lower_frame=overlap_lower_frame,
|
297
|
-
estimated_shifts=estimated_shifts,
|
298
|
-
x_cross_correlation_function=x_cross_correlation_function,
|
299
|
-
y_cross_correlation_function=y_cross_correlation_function,
|
300
|
-
x_shifts_params=x_shifts_params,
|
301
|
-
y_shifts_params=y_shifts_params,
|
302
|
-
)
|
303
|
-
|
304
|
-
|
305
|
-
from nabu.pipeline.estimators import estimate_cor
|
306
|
-
|
307
|
-
|
308
|
-
def find_projections_relative_shifts(
|
309
|
-
upper_scan: TomoScanBase,
|
310
|
-
lower_scan: TomoScanBase,
|
311
|
-
estimated_shifts,
|
312
|
-
flip_ud_upper_frame: bool = False,
|
313
|
-
flip_ud_lower_frame: bool = False,
|
314
|
-
projection_for_shift: Union[int, str] = "middle",
|
315
|
-
invert_order: bool = False,
|
316
|
-
x_cross_correlation_function=None,
|
317
|
-
y_cross_correlation_function=None,
|
318
|
-
x_shifts_params: Optional[dict] = None,
|
319
|
-
y_shifts_params: Optional[dict] = None,
|
320
|
-
) -> tuple:
|
321
|
-
"""
|
322
|
-
deduce the relative shift between the two scans.
|
323
|
-
Expected behavior:
|
324
|
-
* compute expected overlap area from z_translations and (sample) pixel size
|
325
|
-
* call an (optional) cross correlation function from the overlap area to compute the x shift and polish the y shift from `projection_for_shift`
|
326
|
-
|
327
|
-
:param TomoScanBase scan_0:
|
328
|
-
:param TomoScanBase scan_1:
|
329
|
-
:param int axis_0_overlap_px: overlap between the two scans in pixel
|
330
|
-
:param Union[int,str] projection_for_shift: index fo the projection to use (in projection space or in scan space ?. For now in projection) or str. If str must be in (`middle`, `first`, `last`)
|
331
|
-
:param str x_cross_correlation_function: optional method to refine x shift from computing cross correlation. For now valid values are: ("skimage", "nabu-fft")
|
332
|
-
:param str y_cross_correlation_function: optional method to refine y shift from computing cross correlation. For now valid values are: ("skimage", "nabu-fft")
|
333
|
-
:param int minimal_overlap_area_for_cross_correlation: if first approximated overlap shift found from z_translation is lower than this value will fall back on taking the full image for the cross correlation and log a warning
|
334
|
-
:param bool invert_order: are projections inverted between the two scans (case if rotation angle are inverted)
|
335
|
-
:param tuple estimated_shifts: 'a priori' shift estimation
|
336
|
-
:return: relative shift of scan_1 with scan_0 as reference: (y_shift, x_shift)
|
337
|
-
:rtype: tuple
|
338
|
-
|
339
|
-
:warning: this function will flip left-right and up-down frames by default. So it will return shift according to this information
|
340
|
-
"""
|
341
|
-
if x_shifts_params is None:
|
342
|
-
x_shifts_params = {}
|
343
|
-
if y_shifts_params is None:
|
344
|
-
y_shifts_params = {}
|
345
|
-
if estimated_shifts[0] < 0:
|
346
|
-
raise ValueError("y_overlap_px is expected to be stricktly positive")
|
347
|
-
|
348
|
-
x_cross_correlation_function = ShiftAlgorithm.from_value(x_cross_correlation_function)
|
349
|
-
y_cross_correlation_function = ShiftAlgorithm.from_value(y_cross_correlation_function)
|
350
|
-
|
351
|
-
# { handle specific use case (finding shift on scan) - when using nabu COR algorithms (for axis 2)
|
352
|
-
if x_cross_correlation_function in (
|
353
|
-
ShiftAlgorithm.SINO_COARSE_TO_FINE,
|
354
|
-
ShiftAlgorithm.COMPOSITE_COARSE_TO_FINE,
|
355
|
-
ShiftAlgorithm.CENTERED,
|
356
|
-
ShiftAlgorithm.GLOBAL,
|
357
|
-
ShiftAlgorithm.GROWING_WINDOW,
|
358
|
-
ShiftAlgorithm.SLIDING_WINDOW,
|
359
|
-
):
|
360
|
-
cor_options = x_shifts_params.copy()
|
361
|
-
cor_options.pop("img_reg_method", None)
|
362
|
-
# remove all none numeric options because estimate_cor will call 'literal_eval' on them
|
363
|
-
|
364
|
-
upper_scan_dataset_info = HDF5DatasetAnalyzer(
|
365
|
-
location=upper_scan.master_file, extra_options={"hdf5_entry": upper_scan.entry}
|
366
|
-
)
|
367
|
-
update_dataset_info_flats_darks(upper_scan_dataset_info, flatfield_mode=1)
|
368
|
-
|
369
|
-
upper_scan_pos = estimate_cor(
|
370
|
-
method=x_cross_correlation_function.value,
|
371
|
-
dataset_info=upper_scan_dataset_info,
|
372
|
-
cor_options=cor_options,
|
373
|
-
)
|
374
|
-
lower_scan_dataset_info = HDF5DatasetAnalyzer(
|
375
|
-
location=lower_scan.master_file, extra_options={"hdf5_entry": lower_scan.entry}
|
376
|
-
)
|
377
|
-
update_dataset_info_flats_darks(lower_scan_dataset_info, flatfield_mode=1)
|
378
|
-
lower_scan_pos = estimate_cor(
|
379
|
-
method=x_cross_correlation_function.value,
|
380
|
-
dataset_info=lower_scan_dataset_info,
|
381
|
-
cor_options=cor_options,
|
382
|
-
)
|
383
|
-
|
384
|
-
estimated_shifts = tuple(
|
385
|
-
[
|
386
|
-
estimated_shifts[0],
|
387
|
-
(lower_scan_pos - upper_scan_pos),
|
388
|
-
]
|
389
|
-
)
|
390
|
-
x_cross_correlation_function = ShiftAlgorithm.NONE
|
391
|
-
|
392
|
-
# } else we will compute shift from the flat projections
|
393
|
-
|
394
|
-
def get_flat_fielded_proj(
|
395
|
-
scan: TomoScanBase, proj_index: int, reverse: bool, transformation_matrix: Optional[numpy.ndarray]
|
396
|
-
):
|
397
|
-
first_proj_idx = sorted(lower_scan.projections.keys(), reverse=reverse)[proj_index]
|
398
|
-
ff = scan.flat_field_correction(
|
399
|
-
(scan.projections[first_proj_idx],),
|
400
|
-
(first_proj_idx,),
|
401
|
-
)[0]
|
402
|
-
assert ff.ndim == 2, f"expects a single 2D frame. Get something with {ff.ndim} dimensions"
|
403
|
-
if transformation_matrix is not None:
|
404
|
-
assert (
|
405
|
-
transformation_matrix.ndim == 2
|
406
|
-
), f"expects a 2D transformation matrix. Get a {transformation_matrix.ndim} D"
|
407
|
-
if numpy.isclose(transformation_matrix[2, 2], -1):
|
408
|
-
transformation_matrix[2, :] = 0
|
409
|
-
transformation_matrix[0, 2] = 0
|
410
|
-
transformation_matrix[2, 2] = 1
|
411
|
-
ff = numpy.flipud(ff)
|
412
|
-
return ff
|
413
|
-
|
414
|
-
if isinstance(projection_for_shift, str):
|
415
|
-
if projection_for_shift.lower() == "first":
|
416
|
-
projection_for_shift = 0
|
417
|
-
elif projection_for_shift.lower() == "last":
|
418
|
-
projection_for_shift = -1
|
419
|
-
elif projection_for_shift.lower() == "middle":
|
420
|
-
projection_for_shift = len(upper_scan.projections) // 2
|
421
|
-
else:
|
422
|
-
try:
|
423
|
-
projection_for_shift = int(projection_for_shift)
|
424
|
-
except ValueError:
|
425
|
-
raise ValueError(
|
426
|
-
f"{projection_for_shift} cannot be cast to an int and is not one of the possible ('first', 'last', 'middle')"
|
427
|
-
)
|
428
|
-
elif not isinstance(projection_for_shift, (int, numpy.number)):
|
429
|
-
raise TypeError(
|
430
|
-
f"projection_for_shift is expected to be an int. Not {type(projection_for_shift)} - {projection_for_shift}"
|
431
|
-
)
|
432
|
-
|
433
|
-
upper_scan_transformations = list(upper_scan.get_detector_transformations(tuple()))
|
434
|
-
if flip_ud_upper_frame:
|
435
|
-
upper_scan_transformations.append(UDDetTransformation())
|
436
|
-
upper_scan_trans_matrix = build_matrix(upper_scan_transformations)
|
437
|
-
lower_scan_transformations = list(lower_scan.get_detector_transformations(tuple()))
|
438
|
-
if flip_ud_lower_frame:
|
439
|
-
lower_scan_transformations.append(UDDetTransformation())
|
440
|
-
lower_scan_trans_matrix = build_matrix(lower_scan_transformations)
|
441
|
-
upper_proj = get_flat_fielded_proj(
|
442
|
-
upper_scan,
|
443
|
-
projection_for_shift,
|
444
|
-
reverse=False,
|
445
|
-
transformation_matrix=upper_scan_trans_matrix,
|
446
|
-
)
|
447
|
-
lower_proj = get_flat_fielded_proj(
|
448
|
-
lower_scan,
|
449
|
-
projection_for_shift,
|
450
|
-
reverse=invert_order,
|
451
|
-
transformation_matrix=lower_scan_trans_matrix,
|
452
|
-
)
|
453
|
-
|
454
|
-
from nabu.stitching.config import KEY_WINDOW_SIZE # avoid cyclic import
|
455
|
-
|
456
|
-
w_window_size = int(y_shifts_params.get(KEY_WINDOW_SIZE, 400))
|
457
|
-
start_overlap = max(estimated_shifts[0] // 2 - w_window_size // 2, 0)
|
458
|
-
end_overlap = min(estimated_shifts[0] // 2 + w_window_size // 2, min(upper_proj.shape[0], lower_proj.shape[0]))
|
459
|
-
if start_overlap == 0:
|
460
|
-
overlap_upper_frame = upper_proj[-end_overlap:]
|
461
|
-
else:
|
462
|
-
overlap_upper_frame = upper_proj[-end_overlap:-start_overlap]
|
463
|
-
overlap_lower_frame = lower_proj[start_overlap:end_overlap]
|
464
|
-
if not overlap_upper_frame.shape == overlap_lower_frame.shape:
|
465
|
-
raise ValueError(f"Fail to get consistant overlap ({overlap_upper_frame.shape} vs {overlap_lower_frame.shape})")
|
466
|
-
|
467
|
-
return find_frame_relative_shifts(
|
468
|
-
overlap_upper_frame=overlap_upper_frame,
|
469
|
-
overlap_lower_frame=overlap_lower_frame,
|
470
|
-
estimated_shifts=estimated_shifts,
|
471
|
-
x_cross_correlation_function=x_cross_correlation_function,
|
472
|
-
y_cross_correlation_function=y_cross_correlation_function,
|
473
|
-
x_shifts_params=x_shifts_params,
|
474
|
-
y_shifts_params=y_shifts_params,
|
475
|
-
)
|
476
|
-
|
477
|
-
|
478
|
-
def find_shift_correlate(img1, img2, padding_mode="reflect"):
|
479
|
-
alignment = AlignmentBase()
|
480
|
-
cc = alignment._compute_correlation_fft(
|
481
|
-
img1,
|
482
|
-
img2,
|
483
|
-
padding_mode,
|
484
|
-
)
|
485
|
-
|
486
|
-
img_shape = img1.shape[-2:]
|
487
|
-
cc_vs = numpy.fft.fftfreq(img_shape[-2], 1 / img_shape[-2])
|
488
|
-
cc_hs = numpy.fft.fftfreq(img_shape[-1], 1 / img_shape[-1])
|
489
|
-
|
490
|
-
(f_vals, fv, fh) = alignment.extract_peak_region_2d(cc, cc_vs=cc_vs, cc_hs=cc_hs)
|
491
|
-
shifts_vh = alignment.refine_max_position_2d(f_vals, fv, fh)
|
492
|
-
return -shifts_vh
|
493
|
-
|
494
|
-
|
495
|
-
def find_shift_with_itk(img1: numpy.ndarray, img2: numpy.ndarray) -> tuple:
|
496
|
-
# created from https://examples.itk.org/src/registration/common/perform2dtranslationregistrationwithmeansquares/documentation
|
497
|
-
# return (y_shift, x_shift). For now shift are integers as only integer shift are handled.
|
498
|
-
if not img1.dtype == img2.dtype:
|
499
|
-
raise ValueError("the two images are expected to have the same type")
|
500
|
-
if not img1.ndim == img2.ndim == 2:
|
501
|
-
raise ValueError("the two images are expected to 2D numpy arrays")
|
502
|
-
|
503
|
-
if not has_itk:
|
504
|
-
_logger.warning("itk is not installed. Please install it to find shift with it")
|
505
|
-
return (0, 0)
|
506
|
-
|
507
|
-
if StrictVersion(itk.Version.GetITKVersion()) < StrictVersion("4.9.0"):
|
508
|
-
_logger.error("ITK 4.9.0 is required to find shift with it.")
|
509
|
-
return (0, 0)
|
510
|
-
|
511
|
-
pixel_type = itk.ctype("float")
|
512
|
-
img1 = numpy.ascontiguousarray(img1, dtype=numpy.float32)
|
513
|
-
img2 = numpy.ascontiguousarray(img2, dtype=numpy.float32)
|
514
|
-
|
515
|
-
dimension = 2
|
516
|
-
image_type = itk.Image[pixel_type, dimension]
|
517
|
-
|
518
|
-
fixed_image = itk.PyBuffer[image_type].GetImageFromArray(img1)
|
519
|
-
moving_image = itk.PyBuffer[image_type].GetImageFromArray(img2)
|
520
|
-
|
521
|
-
transform_type = itk.TranslationTransform[itk.D, dimension]
|
522
|
-
initial_transform = transform_type.New()
|
523
|
-
|
524
|
-
optimizer = itk.RegularStepGradientDescentOptimizerv4.New(
|
525
|
-
LearningRate=4,
|
526
|
-
MinimumStepLength=0.001,
|
527
|
-
RelaxationFactor=0.5,
|
528
|
-
NumberOfIterations=200,
|
529
|
-
)
|
530
|
-
|
531
|
-
metric = itk.MeanSquaresImageToImageMetricv4[image_type, image_type].New()
|
532
|
-
|
533
|
-
registration = itk.ImageRegistrationMethodv4.New(
|
534
|
-
FixedImage=fixed_image,
|
535
|
-
MovingImage=moving_image,
|
536
|
-
Metric=metric,
|
537
|
-
Optimizer=optimizer,
|
538
|
-
InitialTransform=initial_transform,
|
539
|
-
)
|
540
|
-
|
541
|
-
moving_initial_transform = transform_type.New()
|
542
|
-
initial_parameters = moving_initial_transform.GetParameters()
|
543
|
-
initial_parameters[0] = 0
|
544
|
-
initial_parameters[1] = 0
|
545
|
-
moving_initial_transform.SetParameters(initial_parameters)
|
546
|
-
registration.SetMovingInitialTransform(moving_initial_transform)
|
547
|
-
|
548
|
-
identity_transform = transform_type.New()
|
549
|
-
identity_transform.SetIdentity()
|
550
|
-
registration.SetFixedInitialTransform(identity_transform)
|
551
|
-
|
552
|
-
registration.SetNumberOfLevels(1)
|
553
|
-
registration.SetSmoothingSigmasPerLevel([0])
|
554
|
-
registration.SetShrinkFactorsPerLevel([1])
|
555
|
-
|
556
|
-
registration.Update()
|
557
|
-
|
558
|
-
transform = registration.GetTransform()
|
559
|
-
final_parameters = transform.GetParameters()
|
560
|
-
translation_along_x = final_parameters.GetElement(0)
|
561
|
-
translation_along_y = final_parameters.GetElement(1)
|
562
|
-
|
563
|
-
return numpy.round(translation_along_y), numpy.round(translation_along_x)
|