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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- 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
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"info",
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]
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for method in methods:
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self.__setattr__(method, print)
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LogLevel = {
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"notset": logging.NOTSET,
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"debug": logging.DEBUG,
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"info": logging.INFO,
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"warn": logging.WARN,
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"warning": logging.WARNING,
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"error": logging.ERROR,
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"critical": logging.CRITICAL,
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}
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@@ -1,217 +0,0 @@
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import os
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import numpy as np
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from silx.io.url import DataUrl
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from tomoscan.io import HDF5File
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from tomoscan.esrf.scan.nxtomoscan import NXtomoScan
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from ..utils import check_supported, is_writeable
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def get_frame_possible_urls(dataset_info, user_dir, output_dir, frame_type):
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"""
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Return a list with the possible location of reduced dark/flat frames.
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Parameters
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----------
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dataset_info: DatasetAnalyzer object
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DatasetAnalyzer object: data structure containing information on the parsed dataset
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user_dir: str or None
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User-provided directory location for the reduced frames.
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output_dir: str or None
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Output processing directory
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frame_type: str
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Frame type, can be "flats" or "darks".
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"""
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check_supported(frame_type, ["flats", "darks"], "frame type")
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h5scan = dataset_info.dataset_scanner # tomoscan object
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if frame_type == "flats":
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dataurl_default_template = h5scan.REDUCED_FLATS_DATAURLS[0]
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else:
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dataurl_default_template = h5scan.REDUCED_DARKS_DATAURLS[0]
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def make_dataurl(dirname):
|
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# The template formatting should be done by tomoscan in principle, but this complicates logging.
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rel_file_path = dataurl_default_template.file_path().format(
|
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scan_prefix=dataset_info.dataset_scanner.get_dataset_basename()
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)
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return DataUrl(
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file_path=os.path.join(dirname, rel_file_path),
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data_path=dataurl_default_template.data_path(),
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data_slice=dataurl_default_template.data_slice(), # not sure if needed
|
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scheme="silx",
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)
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urls = {"user": None, "dataset": None, "output": None}
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if user_dir is not None:
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urls["user"] = make_dataurl(user_dir)
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|
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# tomoscan.esrf.scan.hdf5scan.REDUCED_{DARKS|FLATS}_DATAURLS.file_path() is a relative path
|
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# Create a absolute path instead
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urls["dataset"] = make_dataurl(os.path.dirname(h5scan.master_file))
|
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|
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if output_dir is not None:
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urls["output"] = make_dataurl(output_dir)
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|
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return urls
|
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|
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|
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def get_metadata_url(url, frame_type):
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"""
|
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Return the url of the metadata stored alongside flats/darks
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"""
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63
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check_supported(frame_type, ["flats", "darks"], "frame type")
|
64
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template_url = getattr(NXtomoScan, "REDUCED_%s_METADATAURLS" % frame_type.upper())[0]
|
65
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return DataUrl(
|
66
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file_path=url.file_path(),
|
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data_path=template_url.data_path(),
|
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scheme="silx",
|
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)
|
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|
71
|
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|
72
|
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def tomoscan_load_reduced_frames(dataset_info, frame_type, url):
|
73
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tomoscan_method = getattr(dataset_info.dataset_scanner, "load_reduced_%s" % frame_type)
|
74
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return tomoscan_method(
|
75
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inputs_urls=[url],
|
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return_as_url=True,
|
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return_info=True,
|
78
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metadata_input_urls=[get_metadata_url(url, frame_type)],
|
79
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)
|
80
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|
81
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|
82
|
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def tomoscan_save_reduced_frames(dataset_info, frame_type, url, frames, info):
|
83
|
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tomoscan_method = getattr(dataset_info.dataset_scanner, "save_reduced_%s" % frame_type)
|
84
|
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kwargs = {"%s_infos" % frame_type: info, "overwrite": True}
|
85
|
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return tomoscan_method(
|
86
|
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frames, output_urls=[url], metadata_output_urls=[get_metadata_url(url, frame_type)], **kwargs
|
87
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)
|
88
|
-
|
89
|
-
|
90
|
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# pylint: disable=E1136
|
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def update_dataset_info_flats_darks(dataset_info, flatfield_mode, output_dir=None, darks_flats_dir=None):
|
92
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"""
|
93
|
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Update a DatasetAnalyzer object with reduced flats/darks (hereafter "reduced frames").
|
94
|
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|
95
|
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How the reduced frames are loaded/computed/saved will depend on the "flatfield_mode" parameter.
|
96
|
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|
97
|
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The principle is the following:
|
98
|
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(1) Attempt at loading already-computed reduced frames (XXX_darks.h5 and XXX_flats.h5):
|
99
|
-
- First check files in the user-defined directory 'darks_flats_dir'
|
100
|
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- Then try to load from files located alongside the .nx dataset (dataset directory)
|
101
|
-
- Then try to load from output_dir, if provided
|
102
|
-
(2) If loading fails, or flatfield_mode == "force_compute", compute the reduced frames.
|
103
|
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(3) Save these reduced frames
|
104
|
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- Save in darks_flats_dir, if provided by user
|
105
|
-
- Otherwise, save in the data directory (next to the .nx file), if write access OK
|
106
|
-
- Otherwise, save in output directory
|
107
|
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"""
|
108
|
-
if flatfield_mode is False:
|
109
|
-
return
|
110
|
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logger = dataset_info.logger
|
111
|
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frames_types = ["darks", "flats"]
|
112
|
-
|
113
|
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reduced_frames_urls = {}
|
114
|
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for frame_type in frames_types:
|
115
|
-
reduced_frames_urls[frame_type] = get_frame_possible_urls(dataset_info, darks_flats_dir, output_dir, frame_type)
|
116
|
-
|
117
|
-
reduced_frames = dict.fromkeys(frames_types, None)
|
118
|
-
|
119
|
-
#
|
120
|
-
# Try to load frames
|
121
|
-
#
|
122
|
-
def load_reduced_frame(url, frame_type, frames_loaded, reduced_frames):
|
123
|
-
if frames_loaded[frame_type]:
|
124
|
-
return
|
125
|
-
frames, info = tomoscan_load_reduced_frames(dataset_info, frame_type, url)
|
126
|
-
if frames not in (None, {}):
|
127
|
-
dataset_info.logger.info("Loaded %s from %s" % (frame_type, url.file_path()))
|
128
|
-
frames_loaded[frame_type] = True
|
129
|
-
reduced_frames[frame_type] = frames, info
|
130
|
-
else:
|
131
|
-
msg = "Could not load %s from %s" % (frame_type, url.file_path())
|
132
|
-
logger.error(msg)
|
133
|
-
|
134
|
-
frames_loaded = dict.fromkeys(frames_types, False)
|
135
|
-
if flatfield_mode != "force-compute":
|
136
|
-
for load_from in ["user", "dataset", "output"]: # in that order
|
137
|
-
for frame_type in frames_types:
|
138
|
-
url = reduced_frames_urls[frame_type][load_from]
|
139
|
-
if url is None:
|
140
|
-
continue # cannot load from this source (eg. undefined folder)
|
141
|
-
load_reduced_frame(url, frame_type, frames_loaded, reduced_frames)
|
142
|
-
if all(frames_loaded.values()):
|
143
|
-
break
|
144
|
-
|
145
|
-
if not all(frames_loaded.values()) and flatfield_mode == "force-load":
|
146
|
-
raise ValueError("Could not load darks/flats (using 'force-load')")
|
147
|
-
|
148
|
-
#
|
149
|
-
# COMPAT. Keep DataUrl - won't be needed in future versions when pipeline will use FlatField
|
150
|
-
# instead of FlatFieldDataUrl
|
151
|
-
frames_urls = reduced_frames.copy()
|
152
|
-
#
|
153
|
-
|
154
|
-
# Compute reduced frames, if needed
|
155
|
-
#
|
156
|
-
if reduced_frames["flats"] is None:
|
157
|
-
reduced_frames["flats"] = dataset_info.dataset_scanner.compute_reduced_flats(return_info=True)
|
158
|
-
if reduced_frames["darks"] is None:
|
159
|
-
reduced_frames["darks"] = dataset_info.dataset_scanner.compute_reduced_darks(return_info=True)
|
160
|
-
|
161
|
-
if reduced_frames["darks"][0] == {} or reduced_frames["flats"][0] == {}:
|
162
|
-
raise ValueError(
|
163
|
-
"Could not get any reduced flat/dark. This probably means that no already-reduced flats/darks were found and that the dataset itself does not have any flat/dark"
|
164
|
-
)
|
165
|
-
|
166
|
-
#
|
167
|
-
# Save reduced frames
|
168
|
-
#
|
169
|
-
|
170
|
-
def save_reduced_frame(url, frame_type, frames_saved):
|
171
|
-
frames, info = reduced_frames[frame_type]
|
172
|
-
tomoscan_save_reduced_frames(dataset_info, frame_type, url, frames, info)
|
173
|
-
dataset_info.logger.info("Saved reduced %s to %s" % (frame_type, url.file_path()))
|
174
|
-
frames_saved[frame_type] = True
|
175
|
-
|
176
|
-
frames_saved = dict.fromkeys(frames_types, False)
|
177
|
-
if not all(frames_loaded.values()):
|
178
|
-
for save_to in ["user", "dataset", "output"]: # in that order
|
179
|
-
for frame_type in frames_types:
|
180
|
-
if frames_loaded[frame_type]:
|
181
|
-
continue # already loaded
|
182
|
-
url = reduced_frames_urls[frame_type][save_to]
|
183
|
-
if url is None:
|
184
|
-
continue # cannot load from this source (eg. undefined folder)
|
185
|
-
if not is_writeable(os.path.dirname(url.file_path())):
|
186
|
-
continue
|
187
|
-
save_reduced_frame(url, frame_type, frames_saved)
|
188
|
-
# COMPAT.
|
189
|
-
if frames_urls[frame_type] is None:
|
190
|
-
frames_urls[frame_type] = tomoscan_load_reduced_frames(dataset_info, frame_type, url)
|
191
|
-
#
|
192
|
-
if all(frames_saved.values()):
|
193
|
-
break
|
194
|
-
|
195
|
-
dataset_info.flats = frames_urls["flats"][0] # reduced_frames["flats"] # in future versions
|
196
|
-
dataset_info.flats_srcurrent = frames_urls["flats"][1].machine_electric_current
|
197
|
-
# This is an extra check to avoid having more than 1 (reduced) dark.
|
198
|
-
# FlatField only works with exactly 1 (reduced) dark (having more than 1 series of darks makes little sense)
|
199
|
-
# This is normally prevented by tomoscan HDF5FramesReducer, but let's add this extra check
|
200
|
-
darks_ = frames_urls["darks"][0] # reduced_frames["darks"] # in future versions
|
201
|
-
if len(darks_) > 1:
|
202
|
-
dark_idx = sorted(darks_.keys())[0]
|
203
|
-
dataset_info.logger.error("Found more that one series of darks. Keeping only the first one")
|
204
|
-
darks_ = {dark_idx: darks_[dark_idx]}
|
205
|
-
#
|
206
|
-
dataset_info.darks = darks_
|
207
|
-
dataset_info.darks_srcurrent = frames_urls["darks"][1].machine_electric_current
|
208
|
-
|
209
|
-
|
210
|
-
# tomoscan "compute_reduced_XX" is quite slow. If needed, here is an alternative implementation
|
211
|
-
def my_reduce_flats(di):
|
212
|
-
res = {}
|
213
|
-
with HDF5File(di.dataset_hdf5_url.file_path(), "r") as f:
|
214
|
-
for data_slice in di.get_data_slices("flats"):
|
215
|
-
data = f[di.dataset_hdf5_url.data_path()][data_slice.start : data_slice.stop]
|
216
|
-
res[data_slice.start] = np.median(data, axis=0)
|
217
|
-
return res
|
File without changes
|
File without changes
|
@@ -1,104 +0,0 @@
|
|
1
|
-
from os import path
|
2
|
-
from tempfile import mkdtemp
|
3
|
-
from shutil import rmtree
|
4
|
-
import pytest
|
5
|
-
import numpy as np
|
6
|
-
from silx.io import get_data
|
7
|
-
from nxtomo.nxobject.nxdetector import ImageKey
|
8
|
-
from nabu.testutils import generate_nx_dataset
|
9
|
-
from nabu.resources.nxflatfield import update_dataset_info_flats_darks
|
10
|
-
from nabu.resources.dataset_analyzer import HDF5DatasetAnalyzer
|
11
|
-
|
12
|
-
|
13
|
-
test_nxflatfield_scenarios = [
|
14
|
-
{
|
15
|
-
"name": "simple",
|
16
|
-
"flats_pos": [slice(1, 6)],
|
17
|
-
"darks_pos": [slice(0, 1)],
|
18
|
-
"output_dir": None,
|
19
|
-
},
|
20
|
-
{
|
21
|
-
"name": "simple_with_save",
|
22
|
-
"flats_pos": [slice(1, 6)],
|
23
|
-
"darks_pos": [slice(0, 1)],
|
24
|
-
"output_dir": None,
|
25
|
-
},
|
26
|
-
{
|
27
|
-
"name": "multiple_with_save",
|
28
|
-
"flats_pos": [slice(0, 10), slice(30, 40)],
|
29
|
-
"darks_pos": [slice(95, 100)],
|
30
|
-
"output_dir": path.join("{tempdir}", "output_reduced"),
|
31
|
-
},
|
32
|
-
]
|
33
|
-
|
34
|
-
|
35
|
-
# parametrize with fixture and "params=" will launch a new class for each scenario.
|
36
|
-
# the attributes set to "cls" will remain for all the tests done in this class
|
37
|
-
# with the current scenario.
|
38
|
-
@pytest.fixture(scope="class", params=test_nxflatfield_scenarios)
|
39
|
-
def bootstrap(request):
|
40
|
-
cls = request.cls
|
41
|
-
cls.n_projs = 265
|
42
|
-
cls.params = request.param
|
43
|
-
cls.tempdir = mkdtemp(prefix="nabu_")
|
44
|
-
yield
|
45
|
-
rmtree(cls.tempdir)
|
46
|
-
|
47
|
-
|
48
|
-
@pytest.mark.usefixtures("bootstrap")
|
49
|
-
class TestNXFlatField:
|
50
|
-
_reduction_func = {"flats": np.median, "darks": np.mean}
|
51
|
-
|
52
|
-
def get_nx_filename(self):
|
53
|
-
return path.join(self.tempdir, "dataset_" + self.params["name"] + ".nx")
|
54
|
-
|
55
|
-
def get_image_key(self):
|
56
|
-
keys = np.zeros(self.n_projs, np.int32)
|
57
|
-
for what, val in [("flats_pos", ImageKey.FLAT_FIELD.value), ("darks_pos", ImageKey.DARK_FIELD.value)]:
|
58
|
-
for pos in self.params[what]:
|
59
|
-
keys[pos.start : pos.stop] = val
|
60
|
-
return keys
|
61
|
-
|
62
|
-
@staticmethod
|
63
|
-
def check_image_key(dataset_info, frame_type, expected_slices):
|
64
|
-
data_slices = dataset_info.get_data_slices(frame_type)
|
65
|
-
assert set(map(str, data_slices)) == set(map(str, expected_slices))
|
66
|
-
|
67
|
-
def test_nxflatfield(self):
|
68
|
-
dataset_fname = self.get_nx_filename()
|
69
|
-
image_key = self.get_image_key()
|
70
|
-
generate_nx_dataset(dataset_fname, image_key)
|
71
|
-
|
72
|
-
dataset_info = HDF5DatasetAnalyzer(dataset_fname)
|
73
|
-
|
74
|
-
# When parsing a "raw" dataset, flats/darks are a series of images.
|
75
|
-
# dataset_info.flats is a dictionary where each key is the index of the frame.
|
76
|
-
# For example dataset_info.flats.keys() = [10, 11, 12, 13, ..., 19, 1200, 1201, 1202, ..., 1219]
|
77
|
-
for frame_type in ["darks", "flats"]:
|
78
|
-
self.check_image_key(dataset_info, frame_type, self.params[frame_type + "_pos"])
|
79
|
-
|
80
|
-
output_dir = self.params.get("output_dir", None)
|
81
|
-
if output_dir is not None:
|
82
|
-
output_dir = output_dir.format(tempdir=self.tempdir)
|
83
|
-
update_dataset_info_flats_darks(dataset_info, True, output_dir=output_dir)
|
84
|
-
# After reduction (median/mean), the flats/darks are located in another file.
|
85
|
-
# median(series_1) goes to entry/flats/idx1, mean(series_2) goes to entry/flats/idx2, etc.
|
86
|
-
assert set(dataset_info.flats.keys()) == set(s.start for s in self.params["flats_pos"])
|
87
|
-
assert set(dataset_info.darks.keys()) == set(s.start for s in self.params["darks_pos"])
|
88
|
-
|
89
|
-
# Check that the computations were correct
|
90
|
-
# Loads the entire volume in memory ! So keep the data volume small for the tests
|
91
|
-
data_volume = get_data(dataset_info.dataset_hdf5_url)
|
92
|
-
expected_flats = {}
|
93
|
-
for s in self.params["flats_pos"]:
|
94
|
-
expected_flats[s.start] = self._reduction_func["flats"](data_volume[s.start : s.stop], axis=0)
|
95
|
-
expected_darks = {}
|
96
|
-
for s in self.params["darks_pos"]:
|
97
|
-
expected_darks[s.start] = self._reduction_func["darks"](data_volume[s.start : s.stop], axis=0)
|
98
|
-
|
99
|
-
flats = {idx: get_data(dataset_info.flats[idx]) for idx in dataset_info.flats.keys()}
|
100
|
-
for idx in flats.keys():
|
101
|
-
assert np.allclose(flats[idx], expected_flats[idx])
|
102
|
-
darks = {idx: get_data(dataset_info.darks[idx]) for idx in dataset_info.darks.keys()}
|
103
|
-
for idx in darks.keys():
|
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|
-
assert np.allclose(darks[idx], expected_darks[idx])
|
@@ -1,47 +0,0 @@
|
|
1
|
-
import pytest
|
2
|
-
from nabu.utils import compare_dicts
|
3
|
-
from nabu.resources.utils import get_quantities_and_units
|
4
|
-
|
5
|
-
|
6
|
-
class TestUnits:
|
7
|
-
expected_results = {
|
8
|
-
"distance = 1 m ; pixel_size = 2.0 um": {"distance": 1.0, "pixel_size": 2e-6},
|
9
|
-
"distance = 1 m ; pixel_size = 2.6 micrometer": {"distance": 1.0, "pixel_size": 2.6e-6},
|
10
|
-
"distance = 10 m ; pixel_size = 2e-6 m": {"distance": 10, "pixel_size": 2e-6},
|
11
|
-
"distance = .5 m ; pixel_size = 2.6e-4 centimeter": {"distance": 0.5, "pixel_size": 2.6e-6},
|
12
|
-
"distance = 10 cm ; pixel_size = 2.5 micrometer ; energy = 1 ev": {
|
13
|
-
"distance": 0.1,
|
14
|
-
"pixel_size": 2.5e-6,
|
15
|
-
"energy": 1.0e-3,
|
16
|
-
},
|
17
|
-
"distance = 10 cm ; pixel_size = 9.0e-3 millimeter ; energy = 19 kev": {
|
18
|
-
"distance": 0.1,
|
19
|
-
"pixel_size": 9e-6,
|
20
|
-
"energy": 19.0,
|
21
|
-
},
|
22
|
-
}
|
23
|
-
expected_failures = {
|
24
|
-
# typo ("ke" instead of "kev")
|
25
|
-
"distance = 10 cm ; energy = 10 ke": ValueError("Cannot convert: ke"),
|
26
|
-
# No units
|
27
|
-
"distance = 10 ; energy = 10 kev": ValueError("not enough values to unpack (expected 2, got 1)"),
|
28
|
-
# Unit not separated by space
|
29
|
-
"distance = 10m; energy = 10 kev": ValueError("not enough values to unpack (expected 2, got 1)"),
|
30
|
-
# Invalid separator
|
31
|
-
"distance = 10 m, energy = 10 kev": ValueError("too many values to unpack (expected 2)"),
|
32
|
-
}
|
33
|
-
|
34
|
-
def test_conversion(self):
|
35
|
-
for test_str, expected_result in self.expected_results.items():
|
36
|
-
res = get_quantities_and_units(test_str)
|
37
|
-
err_msg = str(
|
38
|
-
"Something wrong with quantities/units extraction from '%s': expected %s, got %s"
|
39
|
-
% (test_str, str(expected_result), str(res))
|
40
|
-
)
|
41
|
-
assert compare_dicts(res, expected_result) is None, err_msg
|
42
|
-
|
43
|
-
def test_valid_input(self):
|
44
|
-
for test_str, expected_failure in self.expected_failures.items():
|
45
|
-
with pytest.raises(type(expected_failure)) as e_info:
|
46
|
-
get_quantities_and_units(test_str)
|
47
|
-
assert e_info.value.args[0] == str(expected_failure)
|
@@ -1,174 +0,0 @@
|
|
1
|
-
from ast import literal_eval
|
2
|
-
import numpy as np
|
3
|
-
from psutil import virtual_memory, cpu_count
|
4
|
-
from pyunitsystem.metricsystem import MetricSystem
|
5
|
-
from pyunitsystem.energysystem import EnergySI
|
6
|
-
|
7
|
-
|
8
|
-
def get_values_from_file(fname, n_values=None, shape=None, sep=None, any_size=False):
|
9
|
-
"""
|
10
|
-
Read a text file and scan the values inside.
|
11
|
-
This function expects one value per line, or values separated with a separator
|
12
|
-
defined with the `sep` parameter.
|
13
|
-
|
14
|
-
Parameters
|
15
|
-
----------
|
16
|
-
fname: str
|
17
|
-
Path of the text file
|
18
|
-
n_values: int, optional
|
19
|
-
If set to a value, this function will check that it scans exactly this
|
20
|
-
number of values.
|
21
|
-
Ignored if `shape` is provided
|
22
|
-
shape: tuple, optional
|
23
|
-
Generalization of n_values for higher dimensions.
|
24
|
-
sep: str, optional
|
25
|
-
Separator between values. Default is white space
|
26
|
-
any_size: bool, optional
|
27
|
-
If set to True, then the parameters 'n_values' and 'shape' are ignored.
|
28
|
-
|
29
|
-
Returns
|
30
|
-
--------
|
31
|
-
arr: numpy.ndarray
|
32
|
-
An array containing the values scanned from the text file
|
33
|
-
"""
|
34
|
-
if not (any_size) and not ((n_values is not None) ^ (shape is not None)):
|
35
|
-
raise ValueError("Please provide either n_values or shape")
|
36
|
-
arr = np.loadtxt(fname, ndmin=1)
|
37
|
-
if (n_values is not None) and (arr.shape[0] != n_values):
|
38
|
-
if any_size:
|
39
|
-
arr = arr[:n_values]
|
40
|
-
else:
|
41
|
-
raise ValueError("Expected %d values, but could get %d values" % (n_values, arr.shape[0]))
|
42
|
-
if (shape is not None) and (arr.shape != shape):
|
43
|
-
if any_size:
|
44
|
-
arr = arr[: shape[0], : shape[1]] # TODO handle more dimensions ?
|
45
|
-
else:
|
46
|
-
raise ValueError("Expected shape %s, but got shape %s" % (shape, arr.shape))
|
47
|
-
return arr
|
48
|
-
|
49
|
-
|
50
|
-
def get_memory_per_node(max_mem, is_percentage=True):
|
51
|
-
"""
|
52
|
-
Get the available memory per node in GB.
|
53
|
-
|
54
|
-
Parameters
|
55
|
-
----------
|
56
|
-
max_mem: float
|
57
|
-
If is_percentage is False, then number is interpreted as an absolute
|
58
|
-
number in GigaBytes.
|
59
|
-
Otherwise, it should be a number between 0 and 100 and is interpreted
|
60
|
-
as a percentage.
|
61
|
-
is_percentage: bool
|
62
|
-
A boolean indicating whether the parameter max_mem is to be interpreted
|
63
|
-
as a percentage of available system memory.
|
64
|
-
"""
|
65
|
-
sys_avail_mem = virtual_memory().available / 1e9
|
66
|
-
if is_percentage:
|
67
|
-
return (max_mem / 100.0) * sys_avail_mem
|
68
|
-
else:
|
69
|
-
return min(max_mem, sys_avail_mem)
|
70
|
-
|
71
|
-
|
72
|
-
def get_threads_per_node(max_threads, is_percentage=True):
|
73
|
-
"""
|
74
|
-
Get the available memory per node in GB.
|
75
|
-
|
76
|
-
Parameters
|
77
|
-
----------
|
78
|
-
max_threads: float
|
79
|
-
If is_percentage is False, then number is interpreted as an absolute
|
80
|
-
number of threads.
|
81
|
-
Otherwise, it should be a number between 0 and 100 and is interpreted
|
82
|
-
as a percentage.
|
83
|
-
is_percentage: bool
|
84
|
-
A boolean indicating whether the parameter max_threads is to be interpreted
|
85
|
-
as a percentage of available system memory.
|
86
|
-
"""
|
87
|
-
sys_n_threads = cpu_count(logical=True)
|
88
|
-
if is_percentage:
|
89
|
-
return (max_threads / 100.0) * sys_n_threads
|
90
|
-
else:
|
91
|
-
return min(max_threads, sys_n_threads)
|
92
|
-
|
93
|
-
|
94
|
-
def extract_parameters(params_str, sep=";"):
|
95
|
-
"""
|
96
|
-
Extract the named parameters from a string.
|
97
|
-
|
98
|
-
Example
|
99
|
-
--------
|
100
|
-
The function can be used as follows:
|
101
|
-
|
102
|
-
>>> extract_parameters("window_width=None; median_filt_shape=(3,3); padding_mode='wrap'")
|
103
|
-
... {'window_width': None, 'median_filt_shape': (3, 3), 'padding_mode': 'wrap'}
|
104
|
-
"""
|
105
|
-
if params_str in ("", None):
|
106
|
-
return {}
|
107
|
-
params_list = params_str.strip(sep).split(sep)
|
108
|
-
res = {}
|
109
|
-
for param_str in params_list:
|
110
|
-
param_name, param_val_str = param_str.strip().split("=")
|
111
|
-
param_name = param_name.strip()
|
112
|
-
param_val_str = param_val_str.strip()
|
113
|
-
param_val = literal_eval(param_val_str)
|
114
|
-
res[param_name] = param_val
|
115
|
-
return res
|
116
|
-
|
117
|
-
|
118
|
-
def compact_parameters(params_dict, sep=";"):
|
119
|
-
"""
|
120
|
-
Compact the parameters from a dict into a string.
|
121
|
-
|
122
|
-
This is the inverse of extract_parameters. It can be used for example in tomwer to convert
|
123
|
-
parameters into a string, for example for cor_options, prior to calling a nabu method which
|
124
|
-
is expecting an argument to be in the form of a string containing options.
|
125
|
-
|
126
|
-
Example
|
127
|
-
--------
|
128
|
-
The function can be used as follows:
|
129
|
-
|
130
|
-
>>> compact_parameters( {"side":"near", "near_pos":300 } )
|
131
|
-
... "side=near; nearpos= 300;"
|
132
|
-
"""
|
133
|
-
if params_dict in ({}, None):
|
134
|
-
return ""
|
135
|
-
|
136
|
-
res = ""
|
137
|
-
for key, val in params_dict.items():
|
138
|
-
res = res + "{key} = {val} " + sep
|
139
|
-
return res
|
140
|
-
|
141
|
-
|
142
|
-
def is_hdf5_extension(ext):
|
143
|
-
return ext.lower() in ["h5", "hdf5", "nx"]
|
144
|
-
|
145
|
-
|
146
|
-
def get_quantities_and_units(string, sep=";"):
|
147
|
-
"""
|
148
|
-
Return a dictionary with quantities as keys, and values in SI.
|
149
|
-
|
150
|
-
Example
|
151
|
-
-------
|
152
|
-
get_quantities_and_units("pixel_size = 1.2 um ; distance = 1 m")
|
153
|
-
Will return
|
154
|
-
{"pixel_size": 1.2e-6, "distance": 1}
|
155
|
-
"""
|
156
|
-
|
157
|
-
result = {}
|
158
|
-
quantities = string.split(sep)
|
159
|
-
for quantity in quantities:
|
160
|
-
quantity_name, value_and_unit = quantity.split("=")
|
161
|
-
quantity_name = quantity_name.strip()
|
162
|
-
value_and_unit = value_and_unit.strip()
|
163
|
-
value, unit = value_and_unit.split()
|
164
|
-
val = float(value)
|
165
|
-
# Convert to SI
|
166
|
-
try:
|
167
|
-
# handle metrics
|
168
|
-
conversion_factor = MetricSystem.from_str(unit).value
|
169
|
-
except ValueError:
|
170
|
-
# handle energies
|
171
|
-
conversion_factor = EnergySI.from_str(unit).value / EnergySI.KILOELECTRONVOLT.value
|
172
|
-
|
173
|
-
result[quantity_name] = val * conversion_factor
|
174
|
-
return result
|
File without changes
|