httomo-backends 0.8.0__tar.gz → 0.9.1__tar.gz
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.
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/PKG-INFO +1 -1
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/methods_database/packages/backends/httomolib/httomolib.yaml +8 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/methods_database/packages/backends/httomolib/httomolib_modules.yaml +1 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/methods_database/packages/backends/httomolibgpu/httomolibgpu.yaml +30 -2
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/methods_database/packages/backends/httomolibgpu/httomolibgpu_modules.yaml +1 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/prep/normalize.py +2 -2
- httomo_backends-0.9.1/httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/prep/phase.py +47 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/methods_database/query.py +10 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/pipelines_full/FBP2d_astra_directive.yaml +4 -2
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/pipelines_full/FBP3d_tomobar_denoising_directive.yaml +5 -3
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/pipelines_full/FBP3d_tomobar_directive.yaml +5 -3
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/pipelines_full/FBP3d_tomobar_noimagesaving_directive.yaml +5 -3
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/pipelines_full/FISTA3d_tomobar_directive.yaml +4 -2
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/pipelines_full/LPRec3d_tomobar_directive.yaml +5 -3
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/pipelines_full/deg360_distortion_FBP3d_tomobar_directive.yaml +5 -3
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/pipelines_full/deg360_paganin_FBP3d_tomobar_directive.yaml +3 -3
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/pipelines_full/sweep_center_FBP3d_tomobar_directive.yaml +3 -1
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/pipelines_full/sweep_paganin_FBP3d_tomobar_directive.yaml +2 -2
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/pipelines_full/titaren_center_pc_FBP3d_resample_directive.yaml +4 -2
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/scripts/yaml_pipelines_generator.py +9 -5
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/scripts/yaml_templates_generator.py +5 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/httomo/httomo.data.hdf.loaders/standard_tomo.yaml +1 -0
- httomo_backends-0.9.1/httomo_backends/yaml_templates/httomolib/httomolib.misc.utils/data_checker.yaml +7 -0
- httomo_backends-0.9.1/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.utils/data_checker.yaml +7 -0
- httomo_backends-0.8.0/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.normalize/normalize.yaml → httomo_backends-0.9.1/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.normalize/dark_flat_field_correction.yaml +1 -4
- httomo_backends-0.9.1/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.normalize/minus_log.yaml +3 -0
- httomo_backends-0.9.1/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.phase/paganin_filter_savu_legacy.yaml +7 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/CGLS3d_tomobar.yaml +0 -1
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/FBP2d_astra.yaml +0 -1
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/FBP3d_tomobar.yaml +0 -1
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/FISTA3d_tomobar.yaml +0 -1
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/LPRec3d_tomobar.yaml +0 -5
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/SIRT3d_tomobar.yaml +0 -1
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends.egg-info/PKG-INFO +1 -1
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends.egg-info/SOURCES.txt +5 -1
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/pyproject.toml +1 -1
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/tests/test_httomolibgpu.py +80 -11
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/tests/test_method_query.py +18 -6
- httomo_backends-0.8.0/httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/prep/phase.py +0 -111
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/LICENSE +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/README.rst +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/__init__.py +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/cufft.py +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/methods_database/__init__.py +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/methods_database/packages/__init__.py +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/methods_database/packages/backends/httomolibgpu/__init__.py +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/__init__.py +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/misc/__init__.py +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/misc/corr.py +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/misc/denoise.py +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/misc/morph.py +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/misc/rescale.py +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/prep/__init__.py +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/prep/stripe.py +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/recon/__init__.py +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/recon/algorithm.py +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/recon/peak_memory_line_profile_hook.py +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/methods_database/packages/backends/tomopy/__init__.py +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/methods_database/packages/backends/tomopy/supporting_funcs/__init__.py +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/methods_database/packages/backends/tomopy/supporting_funcs/misc/__init__.py +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/methods_database/packages/backends/tomopy/supporting_funcs/misc/corr.py +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/methods_database/packages/backends/tomopy/supporting_funcs/prep/__init__.py +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/methods_database/packages/backends/tomopy/supporting_funcs/prep/stripe.py +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/methods_database/packages/backends/tomopy/supporting_funcs/recon/__init__.py +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/methods_database/packages/backends/tomopy/supporting_funcs/recon/algorithm.py +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/methods_database/packages/backends/tomopy/tomopy.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/methods_database/packages/backends/tomopy/tomopy_modules.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/methods_database/packages/httomo.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/pipelines_full/__init__.py +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/pipelines_full/tomopy_gridrec_directive.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/scripts/__init__.py +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/scripts/json_pipelines_generator.py +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/scripts/yaml_unsupported_tomopy_remove.py +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/httomo/__init__.py +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/httomo/httomo.methods/calculate_stats.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/httomo/httomo.methods/save_intermediate_data.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/httomolib/__init__.py +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/httomolib/httomolib.misc.images/save_to_images.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/httomolib/httomolib.misc.morph/data_reducer.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/httomolib/httomolib.misc.rescale/rescale_to_int.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/httomolib/httomolib.misc.segm/binary_thresholding.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/httomolib/httomolib.prep.phase/paganin_filter.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/httomolibgpu/__init__.py +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.corr/median_filter.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.corr/remove_outlier.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.denoise/total_variation_PD.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.denoise/total_variation_ROF.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.morph/data_resampler.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.morph/sino_360_to_180.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.rescale/rescale_to_int.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.alignment/distortion_correction_proj_discorpy.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.phase/paganin_filter.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/raven_filter.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/remove_all_stripe.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/remove_stripe_based_sorting.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/remove_stripe_ti.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.rotation/find_center_360.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.rotation/find_center_pc.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.rotation/find_center_vo.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/__init__.py +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.misc.corr/adjust_range.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.misc.corr/circ_mask.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.misc.corr/gaussian_filter.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.misc.corr/median_filter.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.misc.corr/median_filter3d.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.misc.corr/median_filter_nonfinite.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.misc.corr/remove_nan.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.misc.corr/remove_neg.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.misc.corr/remove_outlier.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.misc.corr/remove_outlier1d.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.misc.corr/remove_outlier3d.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.misc.corr/remove_ring.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.misc.corr/sobel_filter.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.misc.morph/downsample.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.misc.morph/pad.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.misc.morph/sino_360_to_180.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.misc.morph/trim_sinogram.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.misc.morph/upsample.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.prep.alignment/add_jitter.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.prep.alignment/add_noise.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.prep.alignment/align_joint.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.prep.alignment/align_seq.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.prep.alignment/blur_edges.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.prep.alignment/distortion_correction_proj.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.prep.alignment/distortion_correction_sino.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.prep.alignment/scale.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.prep.alignment/shift_images.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.prep.normalize/minus_log.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.prep.normalize/normalize.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.prep.normalize/normalize_bg.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.prep.normalize/normalize_nf.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.prep.normalize/normalize_roi.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.prep.phase/retrieve_phase.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.prep.stripe/remove_all_stripe.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.prep.stripe/remove_dead_stripe.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.prep.stripe/remove_large_stripe.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_based_filtering.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_based_fitting.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_based_interpolation.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_based_sorting.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_fw.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_sf.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_ti.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.prep.stripe/stripes_detect3d.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.prep.stripe/stripes_mask3d.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.recon.algorithm/recon.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.recon.rotation/find_center.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.recon.rotation/find_center_pc.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.recon.rotation/find_center_vo.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.sim.project/add_drift.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.sim.project/add_focal_spot_blur.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.sim.project/add_gaussian.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.sim.project/add_poisson.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.sim.project/add_rings.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.sim.project/add_salt_pepper.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.sim.project/add_zingers.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.sim.project/project.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.sim.project/project2.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/yaml_templates/tomopy/tomopy.sim.project/project3.yaml +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends.egg-info/dependency_links.txt +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends.egg-info/requires.txt +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends.egg-info/top_level.txt +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/setup.cfg +0 -0
- {httomo_backends-0.8.0 → httomo_backends-0.9.1}/tests/test_tomopy.py +0 -0
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Metadata-Version: 2.4
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Name: httomo-backends
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Version: 0.
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Version: 0.9.1
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Summary: Supplementary files for HTTomo backends.
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Author: Garry ODonnell, Jacob Williamson
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Author-email: Daniil Kazantsev <daniil.kazantsev@diamond.ac.uk>, Yousef Moazzam <yousef.moazzam@diamond.ac.uk>, Jessica Verschoyle <jessica.verschoyle@diamond.ac.uk>, Naman Gera <naman.gera@diamond.ac.uk>, scientificsoftware@diamond.ac.uk
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misc:
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utils:
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data_checker:
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pattern: all
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padding: False
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__all__ = [
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#!/usr/bin/env python3
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# -*- coding: utf-8 -*-
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# ---------------------------------------------------------------------------
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# Copyright 2022 Diamond Light Source Ltd.
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#
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# You may obtain a copy of the License at
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#
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#
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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# ---------------------------------------------------------------------------
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# Created By : Tomography Team at DLS <scientificsoftware@diamond.ac.uk>
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# Created Date: 21 September 2023
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# ---------------------------------------------------------------------------
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"""Modules for memory estimation for phase retrieval and phase-contrast enhancement"""
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__all__ = [
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"_calc_memory_bytes_for_slices_paganin_filter_savu_legacy",
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]
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def _calc_memory_bytes_for_slices_paganin_filter(
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**kwargs,
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) -> int:
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return paganin_filter(dims_shape, calc_peak_gpu_mem=True, **kwargs)
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def _calc_memory_bytes_for_slices_paganin_filter_savu_legacy(
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**kwargs,
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) -> int:
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return paganin_filter_savu_legacy(dims_shape, calc_peak_gpu_mem=True, **kwargs)
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)
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- method: find_center_360
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module_path: httomolibgpu.recon.rotation
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- method: sino_360_to_180
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module_path: httomolibgpu.misc.morph
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- method: remove_stripe_based_sorting
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module_path: httomolibgpu.prep.stripe
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- method: minus_log
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module_path: httomolibgpu.prep.normalize
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- method: FBP3d_tomobar
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module_path: httomolibgpu.recon.algorithm
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- method: calculate_stats
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@@ -1,9 +1,9 @@
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- method: standard_tomo
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module_path: httomo.data.hdf.loaders
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- method: dark_flat_field_correction
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module_path: httomolibgpu.prep.normalize
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- method: find_center_360
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module_path: httomolibgpu.recon.rotation
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- method: normalize
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module_path: httomolibgpu.prep.normalize
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module_path: httomolibgpu.recon.rotation
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- method: sino_360_to_180
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module_path: httomolibgpu.misc.morph
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- method: remove_stripe_based_sorting
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- method: standard_tomo
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module_path: httomo.data.hdf.loaders
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- method:
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- method: dark_flat_field_correction
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module_path: httomolibgpu.prep.normalize
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- method: minus_log
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module_path: httomolibgpu.prep.normalize
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- method: FBP3d_tomobar
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module_path: httomolibgpu.recon.algorithm
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sweep_parameter: center
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1
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- method: standard_tomo
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module_path: httomo.data.hdf.loaders
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+
- method: dark_flat_field_correction
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+
module_path: httomolibgpu.prep.normalize
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- method: find_center_vo
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module_path: httomolibgpu.recon.rotation
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- method: normalize
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module_path: httomolibgpu.prep.normalize
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- method: paganin_filter
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module_path: httomolibgpu.prep.phase
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sweep_parameter: ratio_delta_beta
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@@ -1,11 +1,13 @@
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- method: standard_tomo
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module_path: httomo.data.hdf.loaders
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+
- method: dark_flat_field_correction
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4
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+
module_path: httomolibgpu.prep.normalize
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- method: find_center_pc
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4
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module_path: httomolibgpu.recon.rotation
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5
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-
- method: normalize
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module_path: httomolibgpu.prep.normalize
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- method: remove_stripe_ti
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8
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module_path: httomolibgpu.prep.stripe
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9
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+
- method: minus_log
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+
module_path: httomolibgpu.prep.normalize
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- method: FBP3d_tomobar
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module_path: httomolibgpu.recon.algorithm
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- method: data_resampler
|
{httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/scripts/yaml_pipelines_generator.py
RENAMED
|
@@ -94,6 +94,7 @@ def yaml_pipelines_generator(
|
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94
94
|
with open(path_to_pipelines, "r") as file:
|
|
95
95
|
try:
|
|
96
96
|
pipeline_file_content = yaml.load(file)
|
|
97
|
+
# print(f"Loading pipeline: {file.name}") # useful for debugging
|
|
97
98
|
except OSError as e:
|
|
98
99
|
print("loading yaml file with methods failed", e)
|
|
99
100
|
|
|
@@ -227,17 +228,20 @@ def yaml_pipelines_generator(
|
|
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227
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|
indent=0,
|
|
228
229
|
)
|
|
229
230
|
pipeline_full += yaml_template_method
|
|
230
|
-
elif "
|
|
231
|
+
elif "dark_flat_field_correction" in method_name:
|
|
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232
|
pipeline_full.yaml_set_comment_before_after_key(
|
|
232
233
|
i,
|
|
233
|
-
"---
|
|
234
|
+
"--- Flat-field and dark-field projection correction. --- ",
|
|
234
235
|
indent=0,
|
|
235
236
|
)
|
|
236
237
|
pipeline_full += yaml_template_method
|
|
237
|
-
|
|
238
|
-
|
|
239
|
-
|
|
238
|
+
elif "minus_log" in method_name:
|
|
239
|
+
pipeline_full.yaml_set_comment_before_after_key(
|
|
240
|
+
i,
|
|
241
|
+
"--- Negative log is required for reconstruction to convert raw intensity measurements into the line integrals of attenuation. --- ",
|
|
242
|
+
indent=0,
|
|
240
243
|
)
|
|
244
|
+
pipeline_full += yaml_template_method
|
|
241
245
|
elif "phase" in module_name:
|
|
242
246
|
pipeline_full.yaml_set_comment_before_after_key(
|
|
243
247
|
i,
|
{httomo_backends-0.8.0 → httomo_backends-0.9.1}/httomo_backends/scripts/yaml_templates_generator.py
RENAMED
|
@@ -221,6 +221,11 @@ def _get_discard_keys() -> List[str]:
|
|
|
221
221
|
"step_xy",
|
|
222
222
|
"jpeg_quality",
|
|
223
223
|
"watermark_vals",
|
|
224
|
+
"power_of_2_oversampling",
|
|
225
|
+
"power_of_2_cropping",
|
|
226
|
+
"min_mem_usage_filter",
|
|
227
|
+
"min_mem_usage_ifft2",
|
|
228
|
+
"calc_peak_gpu_mem",
|
|
224
229
|
]
|
|
225
230
|
return discard_keys
|
|
226
231
|
|
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
Metadata-Version: 2.4
|
|
2
2
|
Name: httomo-backends
|
|
3
|
-
Version: 0.
|
|
3
|
+
Version: 0.9.1
|
|
4
4
|
Summary: Supplementary files for HTTomo backends.
|
|
5
5
|
Author: Garry ODonnell, Jacob Williamson
|
|
6
6
|
Author-email: Daniil Kazantsev <daniil.kazantsev@diamond.ac.uk>, Yousef Moazzam <yousef.moazzam@diamond.ac.uk>, Jessica Verschoyle <jessica.verschoyle@diamond.ac.uk>, Naman Gera <naman.gera@diamond.ac.uk>, scientificsoftware@diamond.ac.uk
|
|
@@ -67,6 +67,7 @@ httomo_backends/yaml_templates/httomolib/httomolib.misc.images/save_to_images.ya
|
|
|
67
67
|
httomo_backends/yaml_templates/httomolib/httomolib.misc.morph/data_reducer.yaml
|
|
68
68
|
httomo_backends/yaml_templates/httomolib/httomolib.misc.rescale/rescale_to_int.yaml
|
|
69
69
|
httomo_backends/yaml_templates/httomolib/httomolib.misc.segm/binary_thresholding.yaml
|
|
70
|
+
httomo_backends/yaml_templates/httomolib/httomolib.misc.utils/data_checker.yaml
|
|
70
71
|
httomo_backends/yaml_templates/httomolib/httomolib.prep.phase/paganin_filter.yaml
|
|
71
72
|
httomo_backends/yaml_templates/httomolibgpu/__init__.py
|
|
72
73
|
httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.corr/median_filter.yaml
|
|
@@ -76,9 +77,12 @@ httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.denoise/total_vari
|
|
|
76
77
|
httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.morph/data_resampler.yaml
|
|
77
78
|
httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.morph/sino_360_to_180.yaml
|
|
78
79
|
httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.rescale/rescale_to_int.yaml
|
|
80
|
+
httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.utils/data_checker.yaml
|
|
79
81
|
httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.alignment/distortion_correction_proj_discorpy.yaml
|
|
80
|
-
httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.normalize/
|
|
82
|
+
httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.normalize/dark_flat_field_correction.yaml
|
|
83
|
+
httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.normalize/minus_log.yaml
|
|
81
84
|
httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.phase/paganin_filter.yaml
|
|
85
|
+
httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.phase/paganin_filter_savu_legacy.yaml
|
|
82
86
|
httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/raven_filter.yaml
|
|
83
87
|
httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/remove_all_stripe.yaml
|
|
84
88
|
httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/remove_stripe_based_sorting.yaml
|