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/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
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- build/lib/nabu/estimation/cor_sino.py +0 -183
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- 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
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- 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
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- 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
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- 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
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- build/lib/nabu/misc/unsharp_cuda.py +0 -6
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- build/lib/nabu/misc/utils.py +0 -117
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- build/lib/nabu/opencl/kernel.py +0 -135
- build/lib/nabu/opencl/memcpy.py +0 -35
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- 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
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- build/lib/nabu/pipeline/config_validators.py +0 -589
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- 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
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- 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
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- build/lib/nabu/pipeline/helical/__init__.py +0 -0
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- build/lib/nabu/pipeline/helical/filtering.py +0 -246
- build/lib/nabu/pipeline/helical/gridded_accumulator.py +0 -575
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- 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
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- build/lib/nabu/pipeline/helical/tests/test_strategy.py +0 -61
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- 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
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- 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
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- 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
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- 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
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- 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
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- build/lib/nabu/processing/processing_base.py +0 -123
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- build/lib/nabu/processing/tests/__init__.py +0 -0
- build/lib/nabu/processing/tests/test_fft.py +0 -268
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- 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
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- 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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import numpy as np
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from tomoscan.io import HDF5File
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def compare_volumes(fname1, fname2, h5_path, chunk_size, do_stats, stop_at_thresh, clip_outer_circle=False):
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result = None
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shp2 = get_hdf5_dataset_shape(fname2, h5_path)
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result = "Volumes do not have the same shape: %s vs %s" % (shp1, shp2)
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return
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# Compare volumes
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n_steps = ceil(shp1[0] / chunk_size)
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data1 = f1[h5_path][start:end, :, :]
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data2 = f2[h5_path][start:end, :, :]
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abs_diff = np.abs(data1 - data2)
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for j in range(abs_diff.shape[0]):
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abs_diff[j] = clip_circle(abs_diff[j], radius=0.9 * min(abs_diff.shape[1:]))
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coord_argmax = idx_1d_to_3d(np.argmax(abs_diff), data1.shape)
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raise
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def compare_volumes_cli():
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args = parse_params_values(
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CompareVolumesConfig, parser_description="A command-line utility for comparing two volumes."
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)
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fname1 = args["volume1"]
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fname2 = args["volume2"]
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h5_path = args["hdf5_path"]
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entry = args["entry"].strip() or None
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if entry is None:
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entry = get_first_hdf5_entry(fname1)
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h5_path = join(entry, "reconstruction/results/data")
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do_stats = bool(args["statistics"])
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chunk_size = args["chunk_size"]
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stop_at_thresh = args["stop_at"] or None
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if stop_at_thresh is not None:
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stop_at_thresh = float(stop_at_thresh)
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res = compare_volumes(fname1, fname2, h5_path, chunk_size, do_stats, stop_at_thresh)
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if res is not None:
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print(res)
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return 0
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if __name__ == "__main__":
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compare_volumes_cli()
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import logging
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import os
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import sys
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import numpy as np
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import re
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from nabu.resources.dataset_analyzer import HDF5DatasetAnalyzer
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from nabu.pipeline.estimators import CompositeCOREstimator, estimate_cor
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from nabu.resources.nxflatfield import update_dataset_info_flats_darks
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from nabu.resources.utils import extract_parameters
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from nxtomo.application.nxtomo import NXtomo
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from .. import version
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from .cli_configs import CompositeCorConfig
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from .utils import parse_params_values
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from ..utils import DictToObj
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import json
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class NumpyArrayEncoder(json.JSONEncoder):
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def default(self, obj):
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if isinstance(obj, np.ndarray):
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return obj.tolist()
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return json.JSONEncoder.default(self, obj)
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def main(user_args=None):
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"Application to extract with the composite cor finder the center of rotation for a scan or a series of scans"
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if user_args is None:
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user_args = sys.argv[1:]
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args_dict = parse_params_values(
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CompositeCorConfig,
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parser_description=main.__doc__,
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program_version="nabu " + version,
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user_args=user_args,
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)
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composite_cor_entry_point(args_dict)
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# here we have been called by the cli. The return value 0 means OK
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return 0
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def composite_cor_entry_point(args_dict):
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args = DictToObj(args_dict)
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if len(os.path.dirname(args.filename_template)) == 0:
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# To make sure that other utility routines can succesfully deal with path within the current directory
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args.filename_template = os.path.join(".", args.filename_template)
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args.filename_template = os.path.abspath(args.filename_template)
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if args.first_stage is not None:
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if args.num_of_stages is None:
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args.num_of_stages = 1
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# if the first_stage parameter has been given then
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# we are using numbers to form the names of the files.
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# The filename must containe a XX..X substring which will be replaced
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pattern = re.compile("[X]+")
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ps = pattern.findall(args.filename_template)
|
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if len(ps) == 0:
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message = f""" You have specified the "first_stage" parameter, with an integer.
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Therefore the "filename_template" parameter is expected to containe a XX..X subsection
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but none was found in the passed parameter which is {args.filename_template}
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"""
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raise ValueError(message)
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ls = list(map(len, ps))
|
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idx = np.argmax(ls)
|
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|
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args.filename_template = args.filename_template.replace(ps[idx], "{i_stage:" + "0" + str(ls[idx]) + "d}")
|
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if args.num_of_stages is None:
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# this way it works also in the simple case where
|
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# only the filename is provided together with the cor options
|
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num_of_stages = 1
|
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first_stage = 0
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else:
|
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num_of_stages = args.num_of_stages
|
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first_stage = args.first_stage
|
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cor_list = []
|
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for iz in range(first_stage, first_stage + num_of_stages):
|
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if args.num_of_stages is not None:
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nexus_name = args.filename_template.format(i_stage=iz)
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else:
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nexus_name = args.filename_template
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|
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dataset_info = HDF5DatasetAnalyzer(nexus_name, extra_options={"h5_entry": args.entry_name})
|
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|
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update_dataset_info_flats_darks(dataset_info, flatfield_mode=1)
|
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|
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|
88
|
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### JL start ###
|
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# Extract CoR parameters from configuration file
|
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try:
|
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cor_options = extract_parameters(args.cor_options, sep=";")
|
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except Exception as exc:
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msg = "Could not extract parameters from cor_options: %s" % (str(exc))
|
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raise ValueError(msg)
|
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### JL end ###
|
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|
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|
97
|
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# JL start ###
|
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|
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#: next bit will be done in estimate
|
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|
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# if "near_pos" not in args.cor_options:
|
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# scan = NXtomo()
|
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# scan.load(file_path=nexus_name, data_path=args.entry_name)
|
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|
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# estimated_near = scan.instrument.detector.estimated_cor_from_motor
|
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|
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#
|
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|
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# cor_options = args.cor_options + f" ; near_pos = {estimated_near} "
|
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|
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#
|
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|
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# else:
|
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|
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# cor_options = args.cor_options
|
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|
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### JL end ###
|
109
|
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|
110
|
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cor_finder = CompositeCOREstimator(
|
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|
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dataset_info,
|
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|
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oversampling=args.oversampling,
|
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|
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theta_interval=args.theta_interval,
|
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|
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n_subsampling_y=args.n_subsampling_y,
|
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|
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take_log=True,
|
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|
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spike_threshold=0.04,
|
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|
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cor_options=cor_options,
|
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|
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norm_order=1,
|
119
|
-
)
|
120
|
-
|
121
|
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cor_position = cor_finder.find_cor()
|
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|
-
|
123
|
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cor_list.append(cor_position)
|
124
|
-
|
125
|
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cor_list = np.array(cor_list).T
|
126
|
-
|
127
|
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if args.output_file is not None:
|
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|
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output_name = args.output_file
|
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|
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else:
|
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|
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output_name = os.path.splitext(args.filename_template)[0] + "_cors.txt"
|
131
|
-
|
132
|
-
if output_name.endswith(".json"):
|
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|
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with open(output_name, "w") as fp:
|
134
|
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json.dump(
|
135
|
-
dict(rotation_axis_position=cor_list[0], rotation_axis_position_list=cor_list),
|
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|
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fp,
|
137
|
-
indent=4,
|
138
|
-
cls=NumpyArrayEncoder,
|
139
|
-
)
|
140
|
-
else:
|
141
|
-
np.savetxt(
|
142
|
-
output_name,
|
143
|
-
cor_list,
|
144
|
-
)
|
@@ -1,70 +0,0 @@
|
|
1
|
-
from .. import version
|
2
|
-
from os import environ
|
3
|
-
|
4
|
-
import argparse
|
5
|
-
import shutil
|
6
|
-
import os
|
7
|
-
import sys
|
8
|
-
import re
|
9
|
-
import h5py
|
10
|
-
import numpy as np
|
11
|
-
|
12
|
-
|
13
|
-
from ..resources.logger import LoggerOrPrint
|
14
|
-
from .utils import parse_params_values
|
15
|
-
from .cli_configs import CorrectRotConfig
|
16
|
-
from silx.io.dictdump import h5todict
|
17
|
-
|
18
|
-
from nxtomo.application.nxtomo import NXtomo
|
19
|
-
|
20
|
-
import h5py
|
21
|
-
from nabu.utils import DictToObj
|
22
|
-
|
23
|
-
|
24
|
-
def main(user_args=None):
|
25
|
-
"""Applies the correction found by diag_to_rot to a nexus file"""
|
26
|
-
|
27
|
-
if user_args is None:
|
28
|
-
user_args = sys.argv[1:]
|
29
|
-
|
30
|
-
args = DictToObj(
|
31
|
-
parse_params_values(
|
32
|
-
CorrectRotConfig,
|
33
|
-
parser_description=main.__doc__,
|
34
|
-
program_version="nabu " + version,
|
35
|
-
user_args=user_args,
|
36
|
-
)
|
37
|
-
)
|
38
|
-
|
39
|
-
# now we read the results of the diag_to_rot utility, they are in the cor_file parameter
|
40
|
-
# of the cli
|
41
|
-
cor_data = DictToObj(h5todict(args.cor_file, "/"))
|
42
|
-
|
43
|
-
my_cor = cor_data.cor[0]
|
44
|
-
# we will take my_cor as cor at the first angular position
|
45
|
-
# and then we correct the x_translation at the other angles
|
46
|
-
|
47
|
-
# We now load the nexus that we wish to correct
|
48
|
-
nx_tomo = NXtomo().load(args.nexus_source, args.entry_name)
|
49
|
-
|
50
|
-
# The cor_file that we use for correction
|
51
|
-
# is providing us with the z_m that gives for each
|
52
|
-
# cor position found in the cor array the corresponding value of
|
53
|
-
# the translation along z (in meters)
|
54
|
-
z_translation = nx_tomo.sample.z_translation.value
|
55
|
-
z_translation = z_translation - z_translation[0]
|
56
|
-
|
57
|
-
# now we interpolate to find the correction
|
58
|
-
# for each position of the encoders
|
59
|
-
cors = np.interp(z_translation, cor_data.z_m, cor_data.cor)
|
60
|
-
|
61
|
-
# this is the correction
|
62
|
-
x_correction = nx_tomo.instrument.detector.x_pixel_size.value * (cors - my_cor) # we are in meters here
|
63
|
-
|
64
|
-
# and we apply it to the nexus that we have loaded
|
65
|
-
nx_tomo.sample.x_translation = nx_tomo.sample.x_translation.value + x_correction
|
66
|
-
|
67
|
-
# finally we write it to the corrected nexus file
|
68
|
-
nx_tomo.save(file_path=args.nexus_target, data_path=args.entry_name, overwrite=True)
|
69
|
-
|
70
|
-
return 0
|
@@ -1,153 +0,0 @@
|
|
1
|
-
from .. import version
|
2
|
-
import numpy as np
|
3
|
-
import h5py
|
4
|
-
import argparse
|
5
|
-
import sys
|
6
|
-
from .cli_configs import CreateDistortionMapHorizontallyMatchedFromPolyConfig
|
7
|
-
from .utils import parse_params_values
|
8
|
-
from ..utils import DictToObj
|
9
|
-
from ..resources.logger import Logger, LoggerOrPrint
|
10
|
-
|
11
|
-
|
12
|
-
def create_distortion_maps_entry_point(user_args=None):
|
13
|
-
"""This application builds two arrays. Let us call them map_x and map_z. Both are 2D arrays with shape given by (nz, nx).
|
14
|
-
These maps are meant to be used to generate a corrected detector image, using them to obtain the pixel (i,j) of the corrected
|
15
|
-
image by interpolating the raw data at position ( map_z(i,j), map_x(i,j) ).
|
16
|
-
|
17
|
-
This map is determined by a user given polynomial P(rs) in the radial variable rs = sqrt( (z-center_z)**2 + (x-center_x)**2 ) / (nx/2)
|
18
|
-
where center_z and center_x give the center around which the deformation is centered.
|
19
|
-
|
20
|
-
The perfect position (zp,xp) , that would be observed on a perfect detector, of a photon observed at pixel (z,x) of the distorted detector is:
|
21
|
-
|
22
|
-
(zp, xp) = (center_z, center_x) + P(rs) * ( z - center_z , x - center_x )
|
23
|
-
|
24
|
-
The polynomial is given by P(rs) = rs *(1 + c2 * rs**2 + c4 * rs**4)
|
25
|
-
|
26
|
-
The map is rescaled and reshifted so that a perfect match is realised at the borders of a horizontal line passing by the center. This ensures coerence
|
27
|
-
with the procedure of pixel size calibration which is performed moving a needle horizontally and reading the motor positions at the extreme positions.
|
28
|
-
|
29
|
-
The maps are written in the target file, creating it as hdf5 file, in the datasets
|
30
|
-
|
31
|
-
"/coords_source_x"
|
32
|
-
"/coords_source_z"
|
33
|
-
|
34
|
-
The URLs of these two maps can be used for the detector correction of type "map_xz"
|
35
|
-
in the nabu configuration file as in this example
|
36
|
-
|
37
|
-
[dataset]
|
38
|
-
...
|
39
|
-
detector_distortion_correction = map_xz
|
40
|
-
detector_distortion_correction_options = map_x="silx:./map_coordinates.h5?path=/coords_source_x" ; map_z="silx:./map_coordinates.h5?path=/coords_source_z"
|
41
|
-
|
42
|
-
"""
|
43
|
-
|
44
|
-
if user_args is None:
|
45
|
-
user_args = sys.argv[1:]
|
46
|
-
args_dict = parse_params_values(
|
47
|
-
CreateDistortionMapHorizontallyMatchedFromPolyConfig,
|
48
|
-
parser_description=create_maps_x_and_z.__doc__,
|
49
|
-
program_version="nabu " + version,
|
50
|
-
user_args=user_args,
|
51
|
-
)
|
52
|
-
|
53
|
-
logger = Logger("create_distortion_maps", level=user_args["loglevel"], logfile="create_distortion_maps.log")
|
54
|
-
|
55
|
-
coords_source_x, coords_source_z, new_axis_pos = create_maps_x_and_z(args_dict)
|
56
|
-
|
57
|
-
with h5py.File(args_dict["target_file"], "w") as f:
|
58
|
-
f["coords_source_x"] = coords_source_x
|
59
|
-
f["coords_source_z"] = coords_source_z
|
60
|
-
|
61
|
-
if new_axis_pos is not None:
|
62
|
-
logger.info("New axis position at %e it was previously %e " % (new_axis_pos, args_dict["axis_pos"]))
|
63
|
-
|
64
|
-
return 0
|
65
|
-
|
66
|
-
|
67
|
-
def create_maps_x_and_z(args_dict):
|
68
|
-
"""This method is meant for those applications which wants to use the functionalities of the poly2map
|
69
|
-
entry point through a standar python API.
|
70
|
-
The argument arg_dict must contain the keys that you can find in cli_configs.py:
|
71
|
-
CreateDistortionMapHorizontallyMatchedFromPolyConfig
|
72
|
-
Look at this files for variables and their meaning and defaults
|
73
|
-
Parameters::
|
74
|
-
args_dict : dict
|
75
|
-
a dictionary containing keys : center_x, center_z, nz, nx, c2, c4, axis_pos
|
76
|
-
return:
|
77
|
-
max_x, map_z, new_rot_pos
|
78
|
-
|
79
|
-
"""
|
80
|
-
args = DictToObj(args_dict)
|
81
|
-
|
82
|
-
nz, nx = args.nz, args.nx
|
83
|
-
center_x, center_z = (args.center_x, args.center_z)
|
84
|
-
|
85
|
-
c4 = args.c4
|
86
|
-
c2 = args.c2
|
87
|
-
|
88
|
-
polynomial = np.poly1d([c4, 0, c2, 0, 1, 0.0])
|
89
|
-
# change of variable
|
90
|
-
cofv = np.poly1d([1.0 / (nx / 2), 0])
|
91
|
-
polynomial = nx / 2 * polynomial(cofv)
|
92
|
-
|
93
|
-
left_border = 0 - center_x
|
94
|
-
right_border = nx - 1 - center_x
|
95
|
-
|
96
|
-
def get_rescaling_shift(left_border, right_border, polynomial):
|
97
|
-
dl = polynomial(left_border)
|
98
|
-
dr = polynomial(right_border)
|
99
|
-
|
100
|
-
rescaling = (dr - dl) / (right_border - left_border)
|
101
|
-
shift = -left_border * rescaling + dl
|
102
|
-
return rescaling, shift
|
103
|
-
|
104
|
-
final_grid_rescaling, final_grid_shift = get_rescaling_shift(left_border, right_border, polynomial)
|
105
|
-
|
106
|
-
coords_z, coords_x = np.indices([nz, nx])
|
107
|
-
|
108
|
-
coords_z = ((coords_z - center_z) * final_grid_rescaling).astype("d")
|
109
|
-
coords_x = ((coords_x - center_x) * final_grid_rescaling + final_grid_shift).astype("d")
|
110
|
-
|
111
|
-
distances_goal = np.sqrt(coords_z * coords_z + coords_x * coords_x)
|
112
|
-
|
113
|
-
distances_unknown = distances_goal
|
114
|
-
|
115
|
-
pp_deriv = polynomial.deriv()
|
116
|
-
|
117
|
-
# iteratively finding the positions to interpolated at by newton method
|
118
|
-
for i in range(10):
|
119
|
-
errors = polynomial(distances_unknown) - distances_goal
|
120
|
-
derivative = pp_deriv(distances_unknown)
|
121
|
-
distances_unknown = distances_unknown - errors / derivative
|
122
|
-
|
123
|
-
distances_data_sources = distances_unknown
|
124
|
-
|
125
|
-
# avoid 0/0
|
126
|
-
distances_data_sources[distances_goal < 1] = 1
|
127
|
-
distances_goal[distances_goal < 1] = 1
|
128
|
-
|
129
|
-
coords_source_z = coords_z * distances_data_sources / distances_goal + center_z
|
130
|
-
coords_source_x = coords_x * distances_data_sources / distances_goal + center_x
|
131
|
-
|
132
|
-
new_axis_pos = None
|
133
|
-
|
134
|
-
if args.axis_pos is not None:
|
135
|
-
# here we search on the central line a point new_axis_pos
|
136
|
-
# such that
|
137
|
-
# coords_source_x[ i_central_y, nuova_axis_pos ] == axis_pos
|
138
|
-
#
|
139
|
-
n_y, n_x = coords_source_x.shape
|
140
|
-
x_coordinates_central_line = coords_source_x[n_y // 2]
|
141
|
-
|
142
|
-
if np.any(np.less_equal(np.diff(x_coordinates_central_line), 0)):
|
143
|
-
message = """ Error in the coordinates map, the X coordinates are not monotonous on the central line """
|
144
|
-
raise ValueError(message)
|
145
|
-
i1 = np.searchsorted(x_coordinates_central_line, args.axis_pos)
|
146
|
-
i1 = np.clip(i1, 1, n_x - 1)
|
147
|
-
i0 = i1 - 1
|
148
|
-
val0 = x_coordinates_central_line[i0]
|
149
|
-
val1 = x_coordinates_central_line[i1]
|
150
|
-
fract = (args.axis_pos - val0) / (val1 - val0)
|
151
|
-
new_axis_pos = i0 * (1 - fract) + i1 * fract
|
152
|
-
|
153
|
-
return coords_source_x, coords_source_z, new_axis_pos
|