MANIFEST.in
README.rst
setup.cfg
setup.py
install/savu_hpc/savu_installer/environment.yml
install/savu_hpc/savu_installer/version.txt
install/savu_hpc/savu_installer/../conda-recipes/installer.sh
install/savu_hpc/savu_installer/../conda-recipes/h5py/build.sh
install/savu_hpc/savu_installer/../conda-recipes/h5py/meta.yaml
install/savu_hpc/savu_installer/../conda-recipes/hdf5/build.sh
install/savu_hpc/savu_installer/../conda-recipes/hdf5/meta.yaml
install/savu_hpc/savu_installer/../conda-recipes/tomophantom/build.sh
install/savu_hpc/savu_installer/../conda-recipes/tomophantom/meta.yaml
install/tests/local_mpi_cpu_test.sh
install/tests/local_mpi_gpu_test.sh
install/tests/mpi_cpu_test.sh
install/tests/mpi_gpu_test.sh
install/tests/test_setup.sh
plugin_examples/__init__.py
plugin_examples/example_median_filter.py
plugin_examples/plugin_templates/__init__.py
plugin_examples/plugin_templates/general/__init__.py
plugin_examples/plugin_templates/general/plugin_template1.py
plugin_examples/plugin_templates/general/plugin_template10.py
plugin_examples/plugin_templates/general/plugin_template1_with_detailed_notes.py
plugin_examples/plugin_templates/general/plugin_template2.py
plugin_examples/plugin_templates/general/plugin_template3.py
plugin_examples/plugin_templates/general/plugin_template4.py
plugin_examples/plugin_templates/general/plugin_template5.py
plugin_examples/plugin_templates/general/plugin_template6.py
plugin_examples/plugin_templates/general/plugin_template7.py
plugin_examples/plugin_templates/general/plugin_template8.py
plugin_examples/plugin_templates/general/plugin_template9.py
plugin_examples/plugin_templates/iterative/__init__.py
plugin_examples/plugin_templates/iterative/testing_iterative_plugin.py
plugin_examples/plugin_templates/iterative/testing_iterative_plugin2.py
plugin_examples/plugin_templates/iterative/testing_iterative_plugin3.py
plugin_examples/plugin_templates/iterative/testing_iterative_plugin4.py
savu/__init__.py
savu/tomo_recon.py
savu/version.py
savu.egg-info/PKG-INFO
savu.egg-info/SOURCES.txt
savu.egg-info/dependency_links.txt
savu.egg-info/entry_points.txt
savu.egg-info/not-zip-safe
savu.egg-info/top_level.txt
savu/core/__init__.py
savu/core/basic_plugin_runner.py
savu/core/checkpointing.py
savu/core/plugin_runner.py
savu/core/transport_setup.py
savu/core/utils.py
savu/core/transports/__init__.py
savu/core/transports/base_transport.py
savu/core/transports/basic_transport.py
savu/core/transports/dosna_transport.py
savu/core/transports/hdf5_transport.py
savu/data/__init__.py
savu/data/chunking.py
savu/data/experiment_collection.py
savu/data/framework_citations.py
savu/data/meta_data.py
savu/data/plugin_list.py
savu/data/data_structures/__init__.py
savu/data/data_structures/data.py
savu/data/data_structures/data_add_ons.py
savu/data/data_structures/data_create.py
savu/data/data_structures/data_notes.py
savu/data/data_structures/plugin_data.py
savu/data/data_structures/preview.py
savu/data/data_structures/utils.py
savu/data/data_structures/data_types/__init__.py
savu/data/data_structures/data_types/base_type.py
savu/data/data_structures/data_types/data_plus_darks_and_flats.py
savu/data/data_structures/data_types/image_data.py
savu/data/data_structures/data_types/map_3dto4d_h5.py
savu/data/data_structures/data_types/mrc.py
savu/data/data_structures/data_types/replicate.py
savu/data/data_structures/data_types/stitch_data.py
savu/data/transport_data/__init__.py
savu/data/transport_data/base_transport_data.py
savu/data/transport_data/basic_transport_data.py
savu/data/transport_data/dosna_transport_data.py
savu/data/transport_data/hdf5_transport_data.py
savu/data/transport_data/slice_lists.py
savu/plugins/__init__.py
savu/plugins/docstring_parser.py
savu/plugins/plugin.py
savu/plugins/plugin_datasets.py
savu/plugins/plugin_datasets_notes.py
savu/plugins/utils.py
savu/plugins/absorption_corrections/__init__.py
savu/plugins/absorption_corrections/base_absorption_correction.py
savu/plugins/absorption_corrections/mc_near_absorption_correction.py
savu/plugins/alignment/__init__.py
savu/plugins/alignment/projection_shift.py
savu/plugins/alignment/projection_vertical_alignment.py
savu/plugins/alignment/sinogram_alignment.py
savu/plugins/alignment/sinogram_clean.py
savu/plugins/analysis/__init__.py
savu/plugins/analysis/base_analysis.py
savu/plugins/analysis/histogram.py
savu/plugins/analysis/stats.py
savu/plugins/analysis/stxm_analysis.py
savu/plugins/azimuthal_integrators/__init__.py
savu/plugins/azimuthal_integrators/base_azimuthal_integrator.py
savu/plugins/azimuthal_integrators/pyfai_azimuthal_integrator.py
savu/plugins/azimuthal_integrators/pyfai_azimuthal_integrator_separate.py
savu/plugins/azimuthal_integrators/pyfai_azimuthal_integrator_with_bragg_filter.py
savu/plugins/basic_operations/__init__.py
savu/plugins/basic_operations/arithmetic_operations.py
savu/plugins/basic_operations/basic_operations.py
savu/plugins/basic_operations/data_rescale.py
savu/plugins/basic_operations/data_threshold.py
savu/plugins/basic_operations/elementwise_arrays_arithmetics.py
savu/plugins/basic_operations/get_data_statistics.py
savu/plugins/basic_operations/no_process_plugin.py
savu/plugins/basic_operations/value_mask_replacement.py
savu/plugins/centering/__init__.py
savu/plugins/centering/vo_centering.py
savu/plugins/centering/vo_centering_iterative.py
savu/plugins/component_analysis/__init__.py
savu/plugins/component_analysis/base_component_analysis.py
savu/plugins/component_analysis/ica.py
savu/plugins/component_analysis/pca.py
savu/plugins/corrections/__init__.py
savu/plugins/corrections/base_correction.py
savu/plugins/corrections/camera_rot_correction.py
savu/plugins/corrections/convert_360_180_sinogram.py
savu/plugins/corrections/dark_flat_field_correction.py
savu/plugins/corrections/distortion_correction.py
savu/plugins/corrections/monitor_correction.py
savu/plugins/corrections/monitor_correction_nd.py
savu/plugins/corrections/mtf_deconvolution.py
savu/plugins/corrections/subpixel_shift.py
savu/plugins/corrections/time_based_correction.py
savu/plugins/corrections/time_based_plus_drift_correction.py
savu/plugins/corrections/timeseries_field_corrections.py
savu/plugins/corrections/xrd_absorption_approximation.py
savu/plugins/developing/__init__.py
savu/plugins/developing/testing_sino_align.py
savu/plugins/driver/__init__.py
savu/plugins/driver/all_cpus_plugin.py
savu/plugins/driver/base_driver.py
savu/plugins/driver/basic_driver.py
savu/plugins/driver/cpu_plugin.py
savu/plugins/driver/gpu_plugin.py
savu/plugins/driver/iterative_plugin.py
savu/plugins/driver/multi_threaded_plugin.py
savu/plugins/driver/plugin_driver.py
savu/plugins/filters/__init__.py
savu/plugins/filters/band_pass.py
savu/plugins/filters/base_filter.py
savu/plugins/filters/dezinger.py
savu/plugins/filters/dezinger_deprecated.py
savu/plugins/filters/dials_find_spots.py
savu/plugins/filters/find_peaks.py
savu/plugins/filters/fresnel_filter.py
savu/plugins/filters/hilbert_filter.py
savu/plugins/filters/image_interpolation.py
savu/plugins/filters/list_to_projections.py
savu/plugins/filters/paganin_filter.py
savu/plugins/filters/poly_background_estimator.py
savu/plugins/filters/pymca.py
savu/plugins/filters/quantisation_filter.py
savu/plugins/filters/spectrum_crop.py
savu/plugins/filters/strip_background.py
savu/plugins/filters/threshold_filter.py
savu/plugins/filters/umpa.py
savu/plugins/filters/denoising/__init__.py
savu/plugins/filters/denoising/ccpi_denoising_cpu.py
savu/plugins/filters/denoising/ccpi_denoising_cpu_3D.py
savu/plugins/filters/denoising/ccpi_denoising_gpu.py
savu/plugins/filters/denoising/ccpi_denoising_gpu_3D.py
savu/plugins/filters/denoising/denoise_bregman_filter.py
savu/plugins/filters/denoising/median_filter.py
savu/plugins/filters/denoising/median_filter_deprecated.py
savu/plugins/filters/denoising/median_filter_gpu.py
savu/plugins/filters/dezingers/__init__.py
savu/plugins/filters/dezingers/dezinger.py
savu/plugins/filters/dezingers/dezinger_gpu.py
savu/plugins/filters/dezingers/dezinger_simple_deprecated.py
savu/plugins/filters/dezingers/dezinger_sinogram_deprecated.py
savu/plugins/fitters/__init__.py
savu/plugins/fitters/base_fitter.py
savu/plugins/fitters/ral_fit.py
savu/plugins/fitters/reproduce_fit.py
savu/plugins/fitters/simple_fit.py
savu/plugins/kinematics/__init__.py
savu/plugins/kinematics/stage_motion.py
savu/plugins/loaders/__init__.py
savu/plugins/loaders/base_loader.py
savu/plugins/loaders/hdf5_template_loader.py
savu/plugins/loaders/image_template_loader.py
savu/plugins/loaders/multi_savu_loader.py
savu/plugins/loaders/random_hdf5_loader.py
savu/plugins/loaders/savu_nexus_loader.py
savu/plugins/loaders/yaml_converter.py
savu/plugins/loaders/full_field_loaders/__init__.py
savu/plugins/loaders/full_field_loaders/dxchange_loader.py
savu/plugins/loaders/full_field_loaders/image_loader.py
savu/plugins/loaders/full_field_loaders/lfov_loader.py
savu/plugins/loaders/full_field_loaders/mrc_loader.py
savu/plugins/loaders/full_field_loaders/multi_nxtomo_loader.py
savu/plugins/loaders/full_field_loaders/nxtomo_loader.py
savu/plugins/loaders/full_field_loaders/random_3d_tomo_loader.py
savu/plugins/loaders/mapping_loaders/__init__.py
savu/plugins/loaders/mapping_loaders/base_multi_modal_loader.py
savu/plugins/loaders/mapping_loaders/mm_loader.py
savu/plugins/loaders/mapping_loaders/nxfluo_loader.py
savu/plugins/loaders/mapping_loaders/nxmonitor_loader.py
savu/plugins/loaders/mapping_loaders/nxptycho_loader.py
savu/plugins/loaders/mapping_loaders/nxstxm_loader.py
savu/plugins/loaders/mapping_loaders/nxxrd_loader.py
savu/plugins/loaders/mapping_loaders/p2r_fly_scan_detector_loader.py
savu/plugins/loaders/mapping_loaders/txm_loader.py
savu/plugins/loaders/mapping_loaders/i08_loaders/__init__.py
savu/plugins/loaders/mapping_loaders/i08_loaders/i08_fluo_loader.py
savu/plugins/loaders/mapping_loaders/i13_loaders/__init__.py
savu/plugins/loaders/mapping_loaders/i13_loaders/i13_fluo_loader.py
savu/plugins/loaders/mapping_loaders/i13_loaders/i13_ptycho_loader.py
savu/plugins/loaders/mapping_loaders/i13_loaders/i13_speckle_loader.py
savu/plugins/loaders/mapping_loaders/i13_loaders/i13_stxm_loader.py
savu/plugins/loaders/mapping_loaders/i13_loaders/i13_stxm_monitor_loader.py
savu/plugins/loaders/mapping_loaders/i13_loaders/i13_stxm_xrf_loader.py
savu/plugins/loaders/mapping_loaders/i14_loaders/__init__.py
savu/plugins/loaders/mapping_loaders/i14_loaders/i14_fluo_loader.py
savu/plugins/loaders/mapping_loaders/i22_loaders/__init__.py
savu/plugins/loaders/mapping_loaders/i22_loaders/i22_tomo_loader.py
savu/plugins/loaders/templates/__init__.py
savu/plugins/loaders/templates/malcolm_templates/__init__.py
savu/plugins/loaders/utils/__init__.py
savu/plugins/loaders/utils/yaml_utils.py
savu/plugins/missing_data/__init__.py
savu/plugins/ptychography/__init__.py
savu/plugins/ptychography/base_ptycho.py
savu/plugins/ptychography/dummy_ptycho.py
savu/plugins/ptychography/ptypy_batch.py
savu/plugins/ptychography/ptypy_compact.py
savu/plugins/reconstructions/__init__.py
savu/plugins/reconstructions/base_recon.py
savu/plugins/reconstructions/scikitimage_filter_back_projection.py
savu/plugins/reconstructions/scikitimage_sart.py
savu/plugins/reconstructions/simple_recon.py
savu/plugins/reconstructions/tomopy_recon.py
savu/plugins/reconstructions/visual_hulls_recon.py
savu/plugins/reconstructions/astra_recons/__init__.py
savu/plugins/reconstructions/astra_recons/astra_recon_cpu.py
savu/plugins/reconstructions/astra_recons/astra_recon_gpu.py
savu/plugins/reconstructions/astra_recons/base_astra_recon.py
savu/plugins/reconstructions/astra_recons/base_astra_vector_recon.py
savu/plugins/reconstructions/tomobar/__init__.py
savu/plugins/reconstructions/tomobar/tomobar_recon.py
savu/plugins/reconstructions/tomobar/tomobar_recon_3D.py
savu/plugins/reconstructions/tomobar/tomobar_recon_cpu.py
savu/plugins/reshape/__init__.py
savu/plugins/reshape/data_removal.py
savu/plugins/reshape/downsample_filter.py
savu/plugins/reshape/image_stitching.py
savu/plugins/reshape/mipmap.py
savu/plugins/ring_removal/__init__.py
savu/plugins/ring_removal/ccpi_ring_artefact_filter.py
savu/plugins/ring_removal/raven_filter.py
savu/plugins/ring_removal/remove_all_rings.py
savu/plugins/ring_removal/remove_large_rings.py
savu/plugins/ring_removal/remove_unresponsive_and_fluctuating_rings.py
savu/plugins/ring_removal/ring_removal_filtering.py
savu/plugins/ring_removal/ring_removal_fitting.py
savu/plugins/ring_removal/ring_removal_interpolation.py
savu/plugins/ring_removal/ring_removal_normalization.py
savu/plugins/ring_removal/ring_removal_regularization.py
savu/plugins/ring_removal/ring_removal_sorting.py
savu/plugins/ring_removal/ring_removal_waveletfft.py
savu/plugins/savers/__init__.py
savu/plugins/savers/base_image_saver.py
savu/plugins/savers/base_saver.py
savu/plugins/savers/edf_saver.py
savu/plugins/savers/hdf5_saver.py
savu/plugins/savers/image_saver.py
savu/plugins/savers/tiff_saver.py
savu/plugins/savers/xrf_saver.py
savu/plugins/savers/utils/__init__.py
savu/plugins/savers/utils/hdf5_utils.py
savu/plugins/segmentation/__init__.py
savu/plugins/segmentation/evolving_contours/__init__.py
savu/plugins/segmentation/evolving_contours/morph_snakes.py
savu/plugins/segmentation/evolving_contours/morph_snakes3D.py
savu/plugins/segmentation/evolving_contours/region_grow.py
savu/plugins/segmentation/evolving_contours/region_grow3D.py
savu/plugins/segmentation/gaussian_mixtures/__init__.py
savu/plugins/segmentation/gaussian_mixtures/gmm_segment3D.py
savu/plugins/segmentation/geo_distance/__init__.py
savu/plugins/segmentation/geo_distance/geo_distance.py
savu/plugins/segmentation/geo_distance/geo_distance3D.py
savu/plugins/segmentation/masks_initialise/__init__.py
savu/plugins/segmentation/masks_initialise/mask_initialiser.py
savu/plugins/segmentation/morphological_operations/__init__.py
savu/plugins/segmentation/morphological_operations/morph_proc.py
savu/plugins/segmentation/morphological_operations/morph_proc_line.py
savu/plugins/segmentation/morphological_operations/morph_proc_line3D.py
savu/plugins/segmentation/morphological_operations/morph_remove_objects.py
savu/plugins/segmentation/thresholding/__init__.py
savu/plugins/segmentation/thresholding/thresh_segm.py
savu/plugins/simulation/__init__.py
savu/plugins/simulation/tomo_phantom.py
savu/plugins/simulation/tomo_phantom_quantification.py
savu/plugins/stats/__init__.py
savu/plugins/stats/min_and_max.py
savu/plugins/visualisation/__init__.py
savu/plugins/visualisation/ortho_slice.py
savu/test/__init__.py
savu/test/base_checkpoint_test.py
savu/test/test_process_list_utils.py
savu/test/test_utils.py
savu/test/travis/__init__.py
savu/test/travis/framework_tests/__init__.py
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savu/test/travis/framework_tests/checkpoint_test.py
savu/test/travis/framework_tests/chunking_test.py
savu/test/travis/framework_tests/data_test.py
savu/test/travis/framework_tests/max_frames_test.py
savu/test/travis/framework_tests/multiple_datasets_test.py
savu/test/travis/framework_tests/multiple_parameter_process_lists_test.py
savu/test/travis/framework_tests/multiple_parameter_test.py
savu/test/travis/framework_tests/parameters_test.py
savu/test/travis/framework_tests/plugin_coverage_test.py
savu/test/travis/framework_tests/plugin_runner_test.py
savu/test/travis/framework_tests/plugins_util_test.py
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savu/test/travis/plugin_tests/basic_operations_test.py
savu/test/travis/plugin_tests/correction_tests/__init__.py
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savu/test/travis/plugin_tests/correction_tests/subpixel_shift_test.py
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savu/test/travis/plugin_tests/filter_tests/__init__.py
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savu/test/travis/plugin_tests/filter_tests/hilbert_test.py
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savu/test/travis/plugin_tests/filter_tests/sinogram_alignment_test.py
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savu/test/travis/plugin_tests/filter_tests/dezinger/dezinger_test.py
savu/test/travis/plugin_tests/filter_tests/multimodal/__init__.py
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savu/test/travis/plugin_tests/filter_tests/multimodal/simple_fit_test.py
savu/test/travis/plugin_tests/filter_tests/multimodal/spectrum_crop_test.py
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savu/test/travis/plugin_tests/loader_tests/__init__.py
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savu/test/travis/plugin_tests/loader_tests/i22_tomo_test.py
savu/test/travis/plugin_tests/loader_tests/mrc_loader_test.py
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savu/test/travis/plugin_tests/loader_tests/nx_xrd_loader_test.py
savu/test/travis/plugin_tests/loader_tests/savu_nexus_loader_test.py
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savu/test/travis/plugin_tests/loader_tests/tiff_loader_test.py
savu/test/travis/plugin_tests/reconstruction_tests/__init__.py
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savu/test/travis/plugin_tests/reconstruction_tests/fbp_test.py
savu/test/travis/plugin_tests/reconstruction_tests/scikit_image_recon_test.py
savu/test/travis/plugin_tests/reconstruction_tests/tomo_pipeline_preview_test.py
savu/test/travis/plugin_tests/reconstruction_tests/tomobar_recon2d_cpu_test.py
savu/test/travis/plugin_tests/reconstruction_tests/tomopy_recon_test.py
savu/test/travis/plugin_tests/segmentation_tests/__init__.py
savu/test/travis/plugin_tests/segmentation_tests/geo_dist_test.py
savu/test/travis/plugin_tests/segmentation_tests/gmm_test.py
savu/test/travis/plugin_tests/segmentation_tests/mask_initialise_test.py
savu/test/travis/plugin_tests/segmentation_tests/morph_operations_test.py
savu/test/travis/plugin_tests/segmentation_tests/morphproc_line_test.py
savu/test/travis/plugin_tests/segmentation_tests/morphsnakes_test.py
savu/test/travis/plugin_tests/segmentation_tests/regiongrow_test.py
savu/test/travis/plugin_tests/simulation_tests/__init__.py
savu/test/travis/plugin_tests/simulation_tests/tomophantom_test.py
savu/test/travis/process_list_tests/__init__.py
savu/test/travis/process_list_tests/map3dto4d_pipeline_test.py
savu/test/travis/process_list_tests/mapping_3Dto4D.py
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