Index

A

abort() (mantidimaging.eyes_tests.eyes_manager.EyesManager method) add_point() (mantidimaging.core.rotation.data_model.CorTiltDataModel method) Advanced (mantidimaging.core.operations.base_filter.FilterGroup attribute) all (mantidimaging.core.data.dataset.BaseDataset property) (mantidimaging.core.data.dataset.MixedDataset property) (mantidimaging.core.data.dataset.StrictDataset property) all_image_ids (mantidimaging.core.data.dataset.BaseDataset property) allowed_filters() (mantidimaging.core.reconstruct.astra_recon.AstraRecon static method) (mantidimaging.core.reconstruct.base_recon.BaseRecon static method) (mantidimaging.core.reconstruct.tomopy_recon.TomopyRecon static method)

allowed_recon_kwargs() (in module mantidimaging.core.reconstruct.astra_recon) (in module mantidimaging.core.reconstruct.cil_recon) (in module mantidimaging.core.reconstruct.tomopy_recon) angle_in_degrees (mantidimaging.core.rotation.data_model.CorTiltDataModel property) arithmetic() (in module mantidimaging.core.parallel.shared) ArithmeticFilter (class in mantidimaging.core.operations.arithmetic.arithmetic) AstraRecon (class in mantidimaging.core.reconstruct.astra_recon)

B

BaseDataset (class in mantidimaging.core.data.dataset) BaseEyesTest (class in mantidimaging.eyes_tests.base_eyes)

BaseFilter (class in mantidimaging.core.operations.base_filter) BaseRecon (class in mantidimaging.core.reconstruct.base_recon) Basic (mantidimaging.core.operations.base_filter.FilterGroup attribute)

C

calculate_chunksize() (in module mantidimaging.core.parallel.utility) check_data_stack() (in module mantidimaging.helper) check_target() (mantidimaging.eyes_tests.base_eyes.BaseEyesTest method) (mantidimaging.eyes_tests.eyes_manager.EyesManager method) CILRecon (class in mantidimaging.core.reconstruct.cil_recon) CircularMaskFilter (class in mantidimaging.core.operations.circular_mask.circular_mask) clear_points() (mantidimaging.core.rotation.data_model.CorTiltDataModel method) clear_proj180deg() (mantidimaging.core.data.images.Images method) clear_results() (mantidimaging.core.rotation.data_model.CorTiltDataModel method) ClipValuesFilter (class in mantidimaging.core.operations.clip_values.clip_values) close_eyes() (mantidimaging.eyes_tests.eyes_manager.EyesManager method) close_imaging() (mantidimaging.eyes_tests.eyes_manager.EyesManager method) CompareImagesWindowTest (class in mantidimaging.eyes_tests.test_compare_images_window)

copy() (mantidimaging.core.data.images.Images method) copy_roi() (mantidimaging.core.data.images.Images method) cor (mantidimaging.core.rotation.data_model.CorTiltDataModel property) (mantidimaging.core.rotation.data_model.Point attribute) cors (mantidimaging.core.rotation.data_model.CorTiltDataModel property) CorTiltDataModel (class in mantidimaging.core.rotation.data_model) count() (mantidimaging.core.data.images.Images method) counts() (mantidimaging.core.data.images.Images method) create_array() (in module mantidimaging.core.parallel.utility) create_empty_images() (mantidimaging.core.data.images.Images static method) create_loading_parameters_for_file_path() (in module mantidimaging.core.io.loader.loader) create_partial() (in module mantidimaging.core.parallel.shared) CropCoordinatesFilter (class in mantidimaging.core.operations.crop_coords.crop_coords) CudaExecuter (class in mantidimaging.core.gpu.utility)

D

dark_after (mantidimaging.core.data.dataset.StrictDataset attribute) dark_before (mantidimaging.core.data.dataset.StrictDataset attribute) data (mantidimaging.core.data.images.Images property) delete_recons() (mantidimaging.core.data.dataset.BaseDataset method) delete_stack() (mantidimaging.core.data.dataset.BaseDataset method) (mantidimaging.core.data.dataset.MixedDataset method) (mantidimaging.core.data.dataset.StrictDataset method)

deserialize_metadata() (in module mantidimaging.core.operation_history.operations) DivideFilter (class in mantidimaging.core.operations.divide.divide) do_calculate_correlation_err() (in module mantidimaging.core.rotation.polyfit_correlation) do_stack_load_seq() (in module mantidimaging.core.io.loader.stack_loader) dtype (mantidimaging.core.data.images.Images property)

E

empty (mantidimaging.core.rotation.data_model.CorTiltDataModel property) enable_correct_fields_only() (in module mantidimaging.core.operations.flat_fielding.flat_fielding) (in module mantidimaging.core.operations.nan_removal.nan_removal) (in module mantidimaging.core.operations.roi_normalisation.roi_normalisation) enough_memory() (in module mantidimaging.core.parallel.utility) execute() (in module mantidimaging.core.io.loader.img_loader) (in module mantidimaging.core.io.loader.stack_loader) (in module mantidimaging.core.parallel.shared) execute_impl() (in module mantidimaging.core.parallel.utility) execute_single() (in module mantidimaging.core.operations.crop_coords.crop_coords) execute_wrapper() (mantidimaging.core.operations.arithmetic.arithmetic.ArithmeticFilter static method) (mantidimaging.core.operations.base_filter.BaseFilter static method) (mantidimaging.core.operations.circular_mask.circular_mask.CircularMaskFilter static method) (mantidimaging.core.operations.clip_values.clip_values.ClipValuesFilter static method) (mantidimaging.core.operations.crop_coords.crop_coords.CropCoordinatesFilter static method) (mantidimaging.core.operations.divide.divide.DivideFilter static method) (mantidimaging.core.operations.flat_fielding.flat_fielding.FlatFieldFilter static method) (mantidimaging.core.operations.gaussian.gaussian.GaussianFilter static method) (mantidimaging.core.operations.median_filter.median_filter.MedianFilter static method) (mantidimaging.core.operations.monitor_normalisation.monitor_normalisation.MonitorNormalisation static method) (mantidimaging.core.operations.nan_removal.nan_removal.NaNRemovalFilter static method) (mantidimaging.core.operations.outliers.outliers.OutliersFilter static method) (mantidimaging.core.operations.rebin.rebin.RebinFilter static method) (mantidimaging.core.operations.remove_all_stripe.remove_all_stripe.RemoveAllStripesFilter static method) (mantidimaging.core.operations.remove_dead_stripe.remove_dead_stripe.RemoveDeadStripesFilter static method) (mantidimaging.core.operations.remove_large_stripe.remove_large_stripe.RemoveLargeStripesFilter static method) (mantidimaging.core.operations.remove_stripe.stripe_removal.StripeRemovalFilter static method) (mantidimaging.core.operations.remove_stripe_filtering.remove_stripe_filtering.RemoveStripeFilteringFilter static method) (mantidimaging.core.operations.remove_stripe_sorting_fitting.remove_stripe_sorting_fitting.RemoveStripeSortingFittingFilter static method) (mantidimaging.core.operations.rescale.rescale.RescaleFilter static method) (mantidimaging.core.operations.ring_removal.ring_removal.RingRemovalFilter static method) (mantidimaging.core.operations.roi_normalisation.roi_normalisation.RoiNormalisationFilter static method) (mantidimaging.core.operations.rotate_stack.rotate_stack.RotateFilter static method)

eyes_manager (mantidimaging.eyes_tests.base_eyes.BaseEyesTest attribute) EyesManager (class in mantidimaging.eyes_tests.eyes_manager)

F

FileInformation (class in mantidimaging.core.io.loader.loader) filenames (mantidimaging.core.data.images.Images property) (mantidimaging.core.io.loader.loader.FileInformation attribute) FILTER_CLASS (mantidimaging.core.operations.loader.OperationModule attribute) filter_func() (mantidimaging.core.operations.arithmetic.arithmetic.ArithmeticFilter static method) (mantidimaging.core.operations.base_filter.BaseFilter static method) (mantidimaging.core.operations.circular_mask.circular_mask.CircularMaskFilter static method) (mantidimaging.core.operations.clip_values.clip_values.ClipValuesFilter static method) (mantidimaging.core.operations.crop_coords.crop_coords.CropCoordinatesFilter static method) (mantidimaging.core.operations.divide.divide.DivideFilter static method) (mantidimaging.core.operations.flat_fielding.flat_fielding.FlatFieldFilter static method) (mantidimaging.core.operations.gaussian.gaussian.GaussianFilter static method) (mantidimaging.core.operations.median_filter.median_filter.MedianFilter static method) (mantidimaging.core.operations.monitor_normalisation.monitor_normalisation.MonitorNormalisation static method) (mantidimaging.core.operations.nan_removal.nan_removal.NaNRemovalFilter static method) (mantidimaging.core.operations.outliers.outliers.OutliersFilter static method) (mantidimaging.core.operations.rebin.rebin.RebinFilter static method) (mantidimaging.core.operations.remove_all_stripe.remove_all_stripe.RemoveAllStripesFilter static method) (mantidimaging.core.operations.remove_dead_stripe.remove_dead_stripe.RemoveDeadStripesFilter static method) (mantidimaging.core.operations.remove_large_stripe.remove_large_stripe.RemoveLargeStripesFilter static method) (mantidimaging.core.operations.remove_stripe.stripe_removal.StripeRemovalFilter static method) (mantidimaging.core.operations.remove_stripe_filtering.remove_stripe_filtering.RemoveStripeFilteringFilter static method) (mantidimaging.core.operations.remove_stripe_sorting_fitting.remove_stripe_sorting_fitting.RemoveStripeSortingFittingFilter static method) (mantidimaging.core.operations.rescale.rescale.RescaleFilter static method) (mantidimaging.core.operations.ring_removal.ring_removal.RingRemovalFilter static method) (mantidimaging.core.operations.roi_normalisation.roi_normalisation.RoiNormalisationFilter static method) (mantidimaging.core.operations.rotate_stack.rotate_stack.RotateFilter static method) filter_name (mantidimaging.core.operations.arithmetic.arithmetic.ArithmeticFilter attribute) (mantidimaging.core.operations.base_filter.BaseFilter attribute) (mantidimaging.core.operations.circular_mask.circular_mask.CircularMaskFilter attribute) (mantidimaging.core.operations.clip_values.clip_values.ClipValuesFilter attribute) (mantidimaging.core.operations.crop_coords.crop_coords.CropCoordinatesFilter attribute) (mantidimaging.core.operations.divide.divide.DivideFilter attribute) (mantidimaging.core.operations.flat_fielding.flat_fielding.FlatFieldFilter attribute) (mantidimaging.core.operations.gaussian.gaussian.GaussianFilter attribute) (mantidimaging.core.operations.median_filter.median_filter.MedianFilter attribute) (mantidimaging.core.operations.monitor_normalisation.monitor_normalisation.MonitorNormalisation attribute) (mantidimaging.core.operations.nan_removal.nan_removal.NaNRemovalFilter attribute) (mantidimaging.core.operations.outliers.outliers.OutliersFilter attribute) (mantidimaging.core.operations.rebin.rebin.RebinFilter attribute) (mantidimaging.core.operations.remove_all_stripe.remove_all_stripe.RemoveAllStripesFilter attribute) (mantidimaging.core.operations.remove_dead_stripe.remove_dead_stripe.RemoveDeadStripesFilter attribute) (mantidimaging.core.operations.remove_large_stripe.remove_large_stripe.RemoveLargeStripesFilter attribute) (mantidimaging.core.operations.remove_stripe.stripe_removal.StripeRemovalFilter attribute) (mantidimaging.core.operations.remove_stripe_filtering.remove_stripe_filtering.RemoveStripeFilteringFilter attribute) (mantidimaging.core.operations.remove_stripe_sorting_fitting.remove_stripe_sorting_fitting.RemoveStripeSortingFittingFilter attribute) (mantidimaging.core.operations.rescale.rescale.RescaleFilter attribute) (mantidimaging.core.operations.ring_removal.ring_removal.RingRemovalFilter attribute) (mantidimaging.core.operations.roi_normalisation.roi_normalisation.RoiNormalisationFilter attribute) (mantidimaging.core.operations.rotate_stack.rotate_stack.RotateFilter attribute)

filter_single_image() (mantidimaging.core.operations.rescale.rescale.RescaleFilter static method) FilterGroup (class in mantidimaging.core.operations.base_filter) find_180deg_proj() (in module mantidimaging.core.io.utility) find_and_verify_sample_log() (in module mantidimaging.core.io.loader.loader) find_center() (in module mantidimaging.core.rotation.polyfit_correlation) find_cor() (mantidimaging.core.reconstruct.astra_recon.AstraRecon static method) (mantidimaging.core.reconstruct.base_recon.BaseRecon static method) (mantidimaging.core.reconstruct.cil_recon.CILRecon static method) (mantidimaging.core.reconstruct.tomopy_recon.TomopyRecon static method) find_first_file_that_is_possibly_a_sample() (in module mantidimaging.core.io.utility) find_images() (in module mantidimaging.core.io.utility) find_images_in_same_directory() (in module mantidimaging.core.io.utility) find_log() (in module mantidimaging.core.io.utility) find_projection_closest_to_180() (in module mantidimaging.core.io.utility) flat_after (mantidimaging.core.data.dataset.StrictDataset attribute) flat_before (mantidimaging.core.data.dataset.StrictDataset attribute) FlatFieldFilter (class in mantidimaging.core.operations.flat_fielding.flat_fielding) from_serialized() (mantidimaging.core.operation_history.operations.ImageOperation static method) full() (mantidimaging.core.reconstruct.astra_recon.AstraRecon static method) (mantidimaging.core.reconstruct.base_recon.BaseRecon static method) (mantidimaging.core.reconstruct.cil_recon.CILRecon static method) (mantidimaging.core.reconstruct.tomopy_recon.TomopyRecon static method)

G

GaussianFilter (class in mantidimaging.core.operations.gaussian.gaussian) generate_names() (in module mantidimaging.core.io.saver) get_all_cors_from_regression() (mantidimaging.core.rotation.data_model.CorTiltDataModel method) get_candidate_file_extensions() (in module mantidimaging.core.io.utility) get_cor_from_regression() (mantidimaging.core.rotation.data_model.CorTiltDataModel method) get_cores() (in module mantidimaging.core.parallel.utility) get_file_extension() (in module mantidimaging.core.io.utility) get_file_names() (in module mantidimaging.core.io.utility) get_folder_names() (in module mantidimaging.core.io.utility) get_images_from_stack() (mantidimaging.core.operations.base_filter.BaseFilter static method) get_prefix() (in module mantidimaging.core.io.utility) get_reconstructor_for() (in module mantidimaging.core.reconstruct) get_search_range() (in module mantidimaging.core.rotation.polyfit_correlation)

gpu_available() (in module mantidimaging.core.gpu.utility) gradient (mantidimaging.core.rotation.data_model.CorTiltDataModel property) group_name() (mantidimaging.core.operations.base_filter.BaseFilter static method) (mantidimaging.core.operations.crop_coords.crop_coords.CropCoordinatesFilter static method) (mantidimaging.core.operations.flat_fielding.flat_fielding.FlatFieldFilter static method) (mantidimaging.core.operations.outliers.outliers.OutliersFilter static method) (mantidimaging.core.operations.remove_all_stripe.remove_all_stripe.RemoveAllStripesFilter static method) (mantidimaging.core.operations.remove_dead_stripe.remove_dead_stripe.RemoveDeadStripesFilter static method) (mantidimaging.core.operations.remove_large_stripe.remove_large_stripe.RemoveLargeStripesFilter static method) (mantidimaging.core.operations.remove_stripe.stripe_removal.StripeRemovalFilter static method) (mantidimaging.core.operations.remove_stripe_filtering.remove_stripe_filtering.RemoveStripeFilteringFilter static method) (mantidimaging.core.operations.remove_stripe_sorting_fitting.remove_stripe_sorting_fitting.RemoveStripeSortingFittingFilter static method) (mantidimaging.core.operations.roi_normalisation.roi_normalisation.RoiNormalisationFilter static method)

H

h_middle (mantidimaging.core.data.images.Images property) has_proj180deg() (mantidimaging.core.data.images.Images method)

has_results (mantidimaging.core.rotation.data_model.CorTiltDataModel property) height (mantidimaging.core.data.images.Images property)

I

id (mantidimaging.core.data.dataset.BaseDataset property) (mantidimaging.core.data.images.Images property) (mantidimaging.core.data.reconlist.ReconList property) ids (mantidimaging.core.data.reconlist.ReconList property) ImageLoader (class in mantidimaging.core.io.loader.img_loader) ImageOperation (class in mantidimaging.core.operation_history.operations) Images (class in mantidimaging.core.data.images) imaging (mantidimaging.eyes_tests.base_eyes.BaseEyesTest property)

index_as_images() (mantidimaging.core.data.images.Images method) initialise_logging() (in module mantidimaging.helper) inplace1() (in module mantidimaging.core.parallel.shared) inplace2() (in module mantidimaging.core.parallel.shared) inplace3() (in module mantidimaging.core.parallel.shared) inplace_second_2d() (in module mantidimaging.core.parallel.shared) is_sinograms (mantidimaging.core.data.images.Images property) iter_points() (mantidimaging.core.rotation.data_model.CorTiltDataModel method)

K

KernelSpinBox (class in mantidimaging.core.operations.median_filter.median_filter)

L

linear_regression() (mantidimaging.core.rotation.data_model.CorTiltDataModel method) link_histograms (mantidimaging.core.operations.base_filter.BaseFilter attribute) (mantidimaging.core.operations.circular_mask.circular_mask.CircularMaskFilter attribute) (mantidimaging.core.operations.clip_values.clip_values.ClipValuesFilter attribute) (mantidimaging.core.operations.crop_coords.crop_coords.CropCoordinatesFilter attribute) (mantidimaging.core.operations.divide.divide.DivideFilter attribute) (mantidimaging.core.operations.gaussian.gaussian.GaussianFilter attribute) (mantidimaging.core.operations.median_filter.median_filter.MedianFilter attribute) (mantidimaging.core.operations.monitor_normalisation.monitor_normalisation.MonitorNormalisation attribute) (mantidimaging.core.operations.nan_removal.nan_removal.NaNRemovalFilter attribute) (mantidimaging.core.operations.outliers.outliers.OutliersFilter attribute) (mantidimaging.core.operations.rebin.rebin.RebinFilter attribute) (mantidimaging.core.operations.remove_all_stripe.remove_all_stripe.RemoveAllStripesFilter attribute) (mantidimaging.core.operations.remove_dead_stripe.remove_dead_stripe.RemoveDeadStripesFilter attribute) (mantidimaging.core.operations.remove_large_stripe.remove_large_stripe.RemoveLargeStripesFilter attribute) (mantidimaging.core.operations.remove_stripe.stripe_removal.StripeRemovalFilter attribute) (mantidimaging.core.operations.remove_stripe_filtering.remove_stripe_filtering.RemoveStripeFilteringFilter attribute) (mantidimaging.core.operations.remove_stripe_sorting_fitting.remove_stripe_sorting_fitting.RemoveStripeSortingFittingFilter attribute) (mantidimaging.core.operations.ring_removal.ring_removal.RingRemovalFilter attribute) (mantidimaging.core.operations.roi_normalisation.roi_normalisation.RoiNormalisationFilter attribute) (mantidimaging.core.operations.rotate_stack.rotate_stack.RotateFilter attribute)

load() (in module mantidimaging.core.io.loader.loader) load_data() (mantidimaging.core.io.loader.img_loader.ImageLoader method) load_files() (mantidimaging.core.io.loader.img_loader.ImageLoader method) load_filter_packages() (in module mantidimaging.core.operations.loader) load_log() (in module mantidimaging.core.io.loader.loader) load_metadata() (mantidimaging.core.data.images.Images method) load_p() (in module mantidimaging.core.io.loader.loader) load_sample_data() (mantidimaging.core.io.loader.img_loader.ImageLoader method) load_stack() (in module mantidimaging.core.io.loader.loader) LoadDialogTest (class in mantidimaging.eyes_tests.test_load_dialog) (class in mantidimaging.eyes_tests.test_nexus_load_dialog) log_file (mantidimaging.core.data.images.Images property)

M

main() (in module mantidimaging.ipython) (in module mantidimaging.main) MainWindowTest (class in mantidimaging.eyes_tests.test_main_window) make_dirs_if_needed() (in module mantidimaging.core.io.saver) make_name_unique() (mantidimaging.core.data.images.Images method) mantidimaging module mantidimaging.core module mantidimaging.core.data module mantidimaging.core.data.dataset module mantidimaging.core.data.images module mantidimaging.core.data.reconlist module mantidimaging.core.data.utility module mantidimaging.core.gpu module mantidimaging.core.gpu.utility module mantidimaging.core.io module mantidimaging.core.io.loader module mantidimaging.core.io.loader.img_loader module mantidimaging.core.io.loader.loader module mantidimaging.core.io.loader.stack_loader module mantidimaging.core.io.saver module mantidimaging.core.io.utility module mantidimaging.core.net module mantidimaging.core.net.help_pages module mantidimaging.core.operation_history module mantidimaging.core.operation_history.const module mantidimaging.core.operation_history.operations module mantidimaging.core.operations module mantidimaging.core.operations.arithmetic module mantidimaging.core.operations.arithmetic.arithmetic module mantidimaging.core.operations.base_filter module mantidimaging.core.operations.circular_mask module mantidimaging.core.operations.circular_mask.circular_mask module mantidimaging.core.operations.clip_values module mantidimaging.core.operations.clip_values.clip_values module mantidimaging.core.operations.crop_coords module mantidimaging.core.operations.crop_coords.crop_coords module mantidimaging.core.operations.divide module mantidimaging.core.operations.divide.divide module mantidimaging.core.operations.flat_fielding module mantidimaging.core.operations.flat_fielding.flat_fielding module mantidimaging.core.operations.gaussian module mantidimaging.core.operations.gaussian.gaussian module mantidimaging.core.operations.loader module mantidimaging.core.operations.median_filter module mantidimaging.core.operations.median_filter.median_filter module mantidimaging.core.operations.monitor_normalisation module mantidimaging.core.operations.monitor_normalisation.monitor_normalisation module mantidimaging.core.operations.nan_removal module mantidimaging.core.operations.nan_removal.nan_removal module mantidimaging.core.operations.outliers module mantidimaging.core.operations.outliers.outliers module mantidimaging.core.operations.rebin module mantidimaging.core.operations.rebin.rebin module mantidimaging.core.operations.remove_all_stripe module mantidimaging.core.operations.remove_all_stripe.remove_all_stripe module mantidimaging.core.operations.remove_dead_stripe module mantidimaging.core.operations.remove_dead_stripe.remove_dead_stripe module mantidimaging.core.operations.remove_large_stripe module mantidimaging.core.operations.remove_large_stripe.remove_large_stripe module mantidimaging.core.operations.remove_stripe module mantidimaging.core.operations.remove_stripe.stripe_removal module mantidimaging.core.operations.remove_stripe_filtering module mantidimaging.core.operations.remove_stripe_filtering.remove_stripe_filtering module mantidimaging.core.operations.remove_stripe_sorting_fitting module mantidimaging.core.operations.remove_stripe_sorting_fitting.remove_stripe_sorting_fitting module mantidimaging.core.operations.rescale module mantidimaging.core.operations.rescale.rescale module mantidimaging.core.operations.rescale.rescale_test module mantidimaging.core.operations.ring_removal module mantidimaging.core.operations.ring_removal.ring_removal module mantidimaging.core.operations.roi_normalisation module mantidimaging.core.operations.roi_normalisation.roi_normalisation module mantidimaging.core.operations.rotate_stack module mantidimaging.core.operations.rotate_stack.rotate_stack module mantidimaging.core.parallel module mantidimaging.core.parallel.shared module mantidimaging.core.parallel.utility module mantidimaging.core.reconstruct module

mantidimaging.core.reconstruct.astra_recon module mantidimaging.core.reconstruct.base_recon module mantidimaging.core.reconstruct.cil_recon module mantidimaging.core.reconstruct.tomopy_recon module mantidimaging.core.rotation module mantidimaging.core.rotation.data_model module mantidimaging.core.rotation.polyfit_correlation module mantidimaging.eyes_tests module mantidimaging.eyes_tests.base_eyes module mantidimaging.eyes_tests.eyes_manager module mantidimaging.eyes_tests.test_compare_images_window module mantidimaging.eyes_tests.test_load_dialog module mantidimaging.eyes_tests.test_main_window module mantidimaging.eyes_tests.test_nexus_load_dialog module mantidimaging.eyes_tests.test_operations_window module mantidimaging.eyes_tests.test_reconstruct_window module mantidimaging.eyes_tests.test_save_dialog module mantidimaging.eyes_tests.test_welcome_window module mantidimaging.helper module mantidimaging.ipython module mantidimaging.main module mark_cropped() (in module mantidimaging.core.data.utility) median_filter() (mantidimaging.core.gpu.utility.CudaExecuter method) MedianFilter (class in mantidimaging.core.operations.median_filter.median_filter) methods() (in module mantidimaging.core.operations.remove_stripe.stripe_removal) MixedDataset (class in mantidimaging.core.data.dataset) MODES (mantidimaging.core.operations.nan_removal.nan_removal.NaNRemovalFilter attribute) modes() (in module mantidimaging.core.operations.gaussian.gaussian) (in module mantidimaging.core.operations.median_filter.median_filter) (in module mantidimaging.core.operations.outliers.outliers) (in module mantidimaging.core.operations.rebin.rebin) (in module mantidimaging.core.operations.roi_normalisation.roi_normalisation) module mantidimaging mantidimaging.core mantidimaging.core.data mantidimaging.core.data.dataset mantidimaging.core.data.images mantidimaging.core.data.reconlist mantidimaging.core.data.utility mantidimaging.core.gpu mantidimaging.core.gpu.utility mantidimaging.core.io mantidimaging.core.io.loader mantidimaging.core.io.loader.img_loader mantidimaging.core.io.loader.loader mantidimaging.core.io.loader.stack_loader mantidimaging.core.io.saver mantidimaging.core.io.utility mantidimaging.core.net mantidimaging.core.net.help_pages mantidimaging.core.operation_history mantidimaging.core.operation_history.const mantidimaging.core.operation_history.operations mantidimaging.core.operations mantidimaging.core.operations.arithmetic mantidimaging.core.operations.arithmetic.arithmetic mantidimaging.core.operations.base_filter mantidimaging.core.operations.circular_mask mantidimaging.core.operations.circular_mask.circular_mask mantidimaging.core.operations.clip_values mantidimaging.core.operations.clip_values.clip_values mantidimaging.core.operations.crop_coords mantidimaging.core.operations.crop_coords.crop_coords mantidimaging.core.operations.divide mantidimaging.core.operations.divide.divide mantidimaging.core.operations.flat_fielding mantidimaging.core.operations.flat_fielding.flat_fielding mantidimaging.core.operations.gaussian mantidimaging.core.operations.gaussian.gaussian mantidimaging.core.operations.loader mantidimaging.core.operations.median_filter mantidimaging.core.operations.median_filter.median_filter mantidimaging.core.operations.monitor_normalisation mantidimaging.core.operations.monitor_normalisation.monitor_normalisation mantidimaging.core.operations.nan_removal mantidimaging.core.operations.nan_removal.nan_removal mantidimaging.core.operations.outliers mantidimaging.core.operations.outliers.outliers mantidimaging.core.operations.rebin mantidimaging.core.operations.rebin.rebin mantidimaging.core.operations.remove_all_stripe mantidimaging.core.operations.remove_all_stripe.remove_all_stripe mantidimaging.core.operations.remove_dead_stripe mantidimaging.core.operations.remove_dead_stripe.remove_dead_stripe mantidimaging.core.operations.remove_large_stripe mantidimaging.core.operations.remove_large_stripe.remove_large_stripe mantidimaging.core.operations.remove_stripe mantidimaging.core.operations.remove_stripe.stripe_removal mantidimaging.core.operations.remove_stripe_filtering mantidimaging.core.operations.remove_stripe_filtering.remove_stripe_filtering mantidimaging.core.operations.remove_stripe_sorting_fitting mantidimaging.core.operations.remove_stripe_sorting_fitting.remove_stripe_sorting_fitting mantidimaging.core.operations.rescale mantidimaging.core.operations.rescale.rescale mantidimaging.core.operations.rescale.rescale_test mantidimaging.core.operations.ring_removal mantidimaging.core.operations.ring_removal.ring_removal mantidimaging.core.operations.roi_normalisation mantidimaging.core.operations.roi_normalisation.roi_normalisation mantidimaging.core.operations.rotate_stack mantidimaging.core.operations.rotate_stack.rotate_stack mantidimaging.core.parallel mantidimaging.core.parallel.shared mantidimaging.core.parallel.utility mantidimaging.core.reconstruct mantidimaging.core.reconstruct.astra_recon mantidimaging.core.reconstruct.base_recon mantidimaging.core.reconstruct.cil_recon mantidimaging.core.reconstruct.tomopy_recon mantidimaging.core.rotation mantidimaging.core.rotation.data_model mantidimaging.core.rotation.polyfit_correlation mantidimaging.eyes_tests mantidimaging.eyes_tests.base_eyes mantidimaging.eyes_tests.eyes_manager mantidimaging.eyes_tests.test_compare_images_window mantidimaging.eyes_tests.test_load_dialog mantidimaging.eyes_tests.test_main_window mantidimaging.eyes_tests.test_nexus_load_dialog mantidimaging.eyes_tests.test_operations_window mantidimaging.eyes_tests.test_reconstruct_window mantidimaging.eyes_tests.test_save_dialog mantidimaging.eyes_tests.test_welcome_window mantidimaging.helper mantidimaging.ipython mantidimaging.main MonitorNormalisation (class in mantidimaging.core.operations.monitor_normalisation.monitor_normalisation) multiprocessing_necessary() (in module mantidimaging.core.parallel.utility)

N

name (mantidimaging.core.data.dataset.BaseDataset property) (mantidimaging.core.data.images.Images attribute) NaNRemovalFilter (class in mantidimaging.core.operations.nan_removal.nan_removal) negative_log() (mantidimaging.core.reconstruct.base_recon.BaseRecon static method) NO_FILENAME_IMAGE_TITLE_STRING (mantidimaging.core.data.images.Images attribute)

NoGroup (mantidimaging.core.operations.base_filter.FilterGroup attribute) num_images (mantidimaging.core.data.images.Images property) num_points (mantidimaging.core.rotation.data_model.CorTiltDataModel property) num_projections (mantidimaging.core.data.images.Images property) num_sinograms (mantidimaging.core.data.images.Images property)

O

open_help_webpage() (in module mantidimaging.core.net.help_pages) open_user_operation_docs() (in module mantidimaging.core.net.help_pages) OperationModule (class in mantidimaging.core.operations.loader)

OperationsWindowTest (class in mantidimaging.eyes_tests.test_operations_window) ops_to_partials() (in module mantidimaging.core.operation_history.operations) OutliersFilter (class in mantidimaging.core.operations.outliers.outliers)

P

parse_args() (in module mantidimaging.main) pixel_size (mantidimaging.core.data.images.Images property) Point (class in mantidimaging.core.rotation.data_model) point() (mantidimaging.core.rotation.data_model.CorTiltDataModel method) populate_slice_indices() (mantidimaging.core.rotation.data_model.CorTiltDataModel method)

prepare_sinogram() (mantidimaging.core.reconstruct.base_recon.BaseRecon static method) proj180deg (mantidimaging.core.data.dataset.StrictDataset property) (mantidimaging.core.data.images.Images property) projection() (mantidimaging.core.data.images.Images method) projection_angles() (mantidimaging.core.data.images.Images method) projections (mantidimaging.core.data.images.Images property)

R

raise_not_implemented() (in module mantidimaging.core.operations.base_filter) read_in_file_information() (in module mantidimaging.core.io.loader.loader) RebinFilter (class in mantidimaging.core.operations.rebin.rebin) ReconList (class in mantidimaging.core.data.reconlist) ReconstructionWindowTest (class in mantidimaging.eyes_tests.test_reconstruct_window) record_operation() (mantidimaging.core.data.images.Images method) register_gui() (mantidimaging.core.operations.arithmetic.arithmetic.ArithmeticFilter static method) (mantidimaging.core.operations.base_filter.BaseFilter static method) (mantidimaging.core.operations.circular_mask.circular_mask.CircularMaskFilter static method) (mantidimaging.core.operations.clip_values.clip_values.ClipValuesFilter static method) (mantidimaging.core.operations.crop_coords.crop_coords.CropCoordinatesFilter static method) (mantidimaging.core.operations.divide.divide.DivideFilter static method) (mantidimaging.core.operations.flat_fielding.flat_fielding.FlatFieldFilter static method) (mantidimaging.core.operations.gaussian.gaussian.GaussianFilter static method) (mantidimaging.core.operations.median_filter.median_filter.MedianFilter static method) (mantidimaging.core.operations.monitor_normalisation.monitor_normalisation.MonitorNormalisation static method) (mantidimaging.core.operations.nan_removal.nan_removal.NaNRemovalFilter static method) (mantidimaging.core.operations.outliers.outliers.OutliersFilter static method) (mantidimaging.core.operations.rebin.rebin.RebinFilter static method) (mantidimaging.core.operations.remove_all_stripe.remove_all_stripe.RemoveAllStripesFilter static method) (mantidimaging.core.operations.remove_dead_stripe.remove_dead_stripe.RemoveDeadStripesFilter static method) (mantidimaging.core.operations.remove_large_stripe.remove_large_stripe.RemoveLargeStripesFilter static method) (mantidimaging.core.operations.remove_stripe.stripe_removal.StripeRemovalFilter static method) (mantidimaging.core.operations.remove_stripe_filtering.remove_stripe_filtering.RemoveStripeFilteringFilter static method) (mantidimaging.core.operations.remove_stripe_sorting_fitting.remove_stripe_sorting_fitting.RemoveStripeSortingFittingFilter static method) (mantidimaging.core.operations.rescale.rescale.RescaleFilter static method) (mantidimaging.core.operations.ring_removal.ring_removal.RingRemovalFilter static method) (mantidimaging.core.operations.roi_normalisation.roi_normalisation.RoiNormalisationFilter static method) (mantidimaging.core.operations.rotate_stack.rotate_stack.RotateFilter static method)

remove_point() (mantidimaging.core.rotation.data_model.CorTiltDataModel method) RemoveAllStripesFilter (class in mantidimaging.core.operations.remove_all_stripe.remove_all_stripe) RemoveDeadStripesFilter (class in mantidimaging.core.operations.remove_dead_stripe.remove_dead_stripe) RemoveLargeStripesFilter (class in mantidimaging.core.operations.remove_large_stripe.remove_large_stripe) RemoveStripeFilteringFilter (class in mantidimaging.core.operations.remove_stripe_filtering.remove_stripe_filtering) RemoveStripeSortingFittingFilter (class in mantidimaging.core.operations.remove_stripe_sorting_fitting.remove_stripe_sorting_fitting) replace() (mantidimaging.core.data.dataset.BaseDataset method) rescale_single_image() (in module mantidimaging.core.io.saver) RescaleFilter (class in mantidimaging.core.operations.rescale.rescale) return_to_second() (in module mantidimaging.core.parallel.shared) return_to_second_at_i() (in module mantidimaging.core.parallel.shared) return_to_self() (in module mantidimaging.core.parallel.shared) RingRemovalFilter (class in mantidimaging.core.operations.ring_removal.ring_removal) RoiNormalisationFilter (class in mantidimaging.core.operations.roi_normalisation.roi_normalisation) RotateFilter (class in mantidimaging.core.operations.rotate_stack.rotate_stack) rotation_matrix2d() (in module mantidimaging.core.reconstruct.astra_recon)

S

sample (mantidimaging.core.data.dataset.StrictDataset attribute) save() (in module mantidimaging.core.io.saver) save_metadata() (mantidimaging.core.data.images.Images method) SaveDialogTest (class in mantidimaging.eyes_tests.test_save_dialog) serialize() (mantidimaging.core.operation_history.operations.ImageOperation method) set_batch() (mantidimaging.eyes_tests.eyes_manager.EyesManager method) set_cor_at_slice() (mantidimaging.core.rotation.data_model.CorTiltDataModel method) set_match_level() (mantidimaging.eyes_tests.eyes_manager.EyesManager method) set_point() (mantidimaging.core.rotation.data_model.CorTiltDataModel method) set_precalculated() (mantidimaging.core.rotation.data_model.CorTiltDataModel method) set_projection_angles() (mantidimaging.core.data.images.Images method) set_up_TV_regularisation() (mantidimaging.core.reconstruct.cil_recon.CILRecon static method) setUp() (mantidimaging.eyes_tests.base_eyes.BaseEyesTest method) (mantidimaging.eyes_tests.test_main_window.MainWindowTest method) (mantidimaging.eyes_tests.test_operations_window.OperationsWindowTest method) (mantidimaging.eyes_tests.test_reconstruct_window.ReconstructionWindowTest method) (mantidimaging.eyes_tests.test_welcome_window.WelcomeWindowTest method) setUpClass() (mantidimaging.eyes_tests.base_eyes.BaseEyesTest class method) shape (mantidimaging.core.io.loader.loader.FileInformation attribute) show_menu() (mantidimaging.eyes_tests.base_eyes.BaseEyesTest static method)

show_negative_overlay (mantidimaging.core.operations.base_filter.BaseFilter attribute) (mantidimaging.core.operations.ring_removal.ring_removal.RingRemovalFilter attribute) single_sino() (mantidimaging.core.reconstruct.astra_recon.AstraRecon static method) (mantidimaging.core.reconstruct.base_recon.BaseRecon static method) (mantidimaging.core.reconstruct.cil_recon.CILRecon static method) (mantidimaging.core.reconstruct.tomopy_recon.TomopyRecon static method) sino() (mantidimaging.core.data.images.Images method) sinograms (mantidimaging.core.data.dataset.BaseDataset property) (mantidimaging.core.data.images.Images property) (mantidimaging.core.io.loader.loader.FileInformation attribute) slice_index (mantidimaging.core.rotation.data_model.Point attribute) slices (mantidimaging.core.rotation.data_model.CorTiltDataModel property) sort_points() (mantidimaging.core.rotation.data_model.CorTiltDataModel method) stack_properties (mantidimaging.core.rotation.data_model.CorTiltDataModel property) stacks (mantidimaging.core.data.reconlist.ReconList property) start_imaging() (mantidimaging.eyes_tests.eyes_manager.EyesManager method) StrictDataset (class in mantidimaging.core.data.dataset) StripeRemovalFilter (class in mantidimaging.core.operations.remove_stripe.stripe_removal) supported_formats() (in module mantidimaging.core.io.loader.loader) sv_params() (mantidimaging.core.operations.base_filter.BaseFilter static method)

T

tearDown() (mantidimaging.eyes_tests.base_eyes.BaseEyesTest method) (mantidimaging.eyes_tests.test_operations_window.OperationsWindowTest method) (mantidimaging.eyes_tests.test_reconstruct_window.ReconstructionWindowTest method) tearDownClass() (mantidimaging.eyes_tests.base_eyes.BaseEyesTest class method) test_about_window_bad_conda() (mantidimaging.eyes_tests.test_welcome_window.WelcomeWindowTest method) test_about_window_bad_cuda() (mantidimaging.eyes_tests.test_welcome_window.WelcomeWindowTest method) test_about_window_good_conda() (mantidimaging.eyes_tests.test_welcome_window.WelcomeWindowTest method) test_about_window_good_cuda() (mantidimaging.eyes_tests.test_welcome_window.WelcomeWindowTest method) test_compare_images_window_opens() (mantidimaging.eyes_tests.test_compare_images_window.CompareImagesWindowTest method) test_execute_wrapper_no_preset() (in module mantidimaging.core.operations.rescale.rescale_test) test_execute_wrapper_with_preset() (in module mantidimaging.core.operations.rescale.rescale_test) test_load_dialog_opens() (mantidimaging.eyes_tests.test_load_dialog.LoadDialogTest method) (mantidimaging.eyes_tests.test_nexus_load_dialog.LoadDialogTest method) test_load_dialog_selected_dataset() (mantidimaging.eyes_tests.test_load_dialog.LoadDialogTest method) test_load_nexus_file_creates_stack() (mantidimaging.eyes_tests.test_nexus_load_dialog.LoadDialogTest method) test_load_nexus_file_populates_window() (mantidimaging.eyes_tests.test_nexus_load_dialog.LoadDialogTest method) test_main_window_file_menu() (mantidimaging.eyes_tests.test_main_window.MainWindowTest method) test_main_window_file_menu_image_loaded() (mantidimaging.eyes_tests.test_main_window.MainWindowTest method) test_main_window_help_menu() (mantidimaging.eyes_tests.test_main_window.MainWindowTest method) test_main_window_image_menu() (mantidimaging.eyes_tests.test_main_window.MainWindowTest method) test_main_window_loaded_2_sets_of_data() (mantidimaging.eyes_tests.test_main_window.MainWindowTest method) test_main_window_loaded_data() (mantidimaging.eyes_tests.test_main_window.MainWindowTest method) test_main_window_opens() (mantidimaging.eyes_tests.test_main_window.MainWindowTest method) test_main_window_opens_image_loaded() (mantidimaging.eyes_tests.test_main_window.MainWindowTest method) test_main_window_workflow_menu() (mantidimaging.eyes_tests.test_main_window.MainWindowTest method) test_main_window_workflow_menu_image_loaded() (mantidimaging.eyes_tests.test_main_window.MainWindowTest method) test_negative_nan_overlay() (mantidimaging.eyes_tests.test_reconstruct_window.ReconstructionWindowTest method) test_operation_window_after_data_was_processed() (mantidimaging.eyes_tests.test_operations_window.OperationsWindowTest method) test_operation_window_opens() (mantidimaging.eyes_tests.test_operations_window.OperationsWindowTest method) test_operation_window_opens_with_data() (mantidimaging.eyes_tests.test_operations_window.OperationsWindowTest method) test_operations_arithmetic_parameters() (mantidimaging.eyes_tests.test_operations_window.OperationsWindowTest method) test_operations_circular_mask_parameters() (mantidimaging.eyes_tests.test_operations_window.OperationsWindowTest method) test_operations_clip_values_parameters() (mantidimaging.eyes_tests.test_operations_window.OperationsWindowTest method)

test_operations_crop_coordinates_parameters() (mantidimaging.eyes_tests.test_operations_window.OperationsWindowTest method) test_operations_divide_parameters() (mantidimaging.eyes_tests.test_operations_window.OperationsWindowTest method) test_operations_flat_fielding_parameters() (mantidimaging.eyes_tests.test_operations_window.OperationsWindowTest method) test_operations_gaussian_parameters() (mantidimaging.eyes_tests.test_operations_window.OperationsWindowTest method) test_operations_median_parameters() (mantidimaging.eyes_tests.test_operations_window.OperationsWindowTest method) test_operations_monitor_normalisation_parameters() (mantidimaging.eyes_tests.test_operations_window.OperationsWindowTest method) test_operations_nan_removal_parameters() (mantidimaging.eyes_tests.test_operations_window.OperationsWindowTest method) test_operations_rebin_parameters() (mantidimaging.eyes_tests.test_operations_window.OperationsWindowTest method) test_operations_remove_all_stripes_parameters() (mantidimaging.eyes_tests.test_operations_window.OperationsWindowTest method) test_operations_remove_dead_stripes_parameters() (mantidimaging.eyes_tests.test_operations_window.OperationsWindowTest method) test_operations_remove_large_stripes_parameters() (mantidimaging.eyes_tests.test_operations_window.OperationsWindowTest method) test_operations_remove_outliers_parameters() (mantidimaging.eyes_tests.test_operations_window.OperationsWindowTest method) test_operations_remove_stripes_with_filtering_parameters() (mantidimaging.eyes_tests.test_operations_window.OperationsWindowTest method) test_operations_remove_stripes_with_sorting_and_fitting_parameters() (mantidimaging.eyes_tests.test_operations_window.OperationsWindowTest method) test_operations_rescale_parameters() (mantidimaging.eyes_tests.test_operations_window.OperationsWindowTest method) test_operations_ring_removal_parameters() (mantidimaging.eyes_tests.test_operations_window.OperationsWindowTest method) test_operations_ROI_normalisation_parameters() (mantidimaging.eyes_tests.test_operations_window.OperationsWindowTest method) test_operations_rotate_stack_parameters() (mantidimaging.eyes_tests.test_operations_window.OperationsWindowTest method) test_operations_stripe_removal_parameters() (mantidimaging.eyes_tests.test_operations_window.OperationsWindowTest method) test_reconstruction_window_colour_palette_dialog() (mantidimaging.eyes_tests.test_reconstruct_window.ReconstructionWindowTest method) test_reconstruction_window_cor_and_tilt_tab() (mantidimaging.eyes_tests.test_reconstruct_window.ReconstructionWindowTest method) test_reconstruction_window_opens() (mantidimaging.eyes_tests.test_reconstruct_window.ReconstructionWindowTest method) test_reconstruction_window_opens_with_data() (mantidimaging.eyes_tests.test_reconstruct_window.ReconstructionWindowTest method) test_reconstruction_window_reconstruct_tab() (mantidimaging.eyes_tests.test_reconstruct_window.ReconstructionWindowTest method) test_rescale() (in module mantidimaging.core.operations.rescale.rescale_test) test_rescale_ignores_nans() (in module mantidimaging.core.operations.rescale.rescale_test) test_save_dialog_opens_with_dataset() (mantidimaging.eyes_tests.test_save_dialog.SaveDialogTest method) test_save_dialog_opens_with_no_dataset() (mantidimaging.eyes_tests.test_save_dialog.SaveDialogTest method) test_scale_single_image() (in module mantidimaging.core.operations.rescale.rescale_test) test_scale_single_image_bad_offset() (in module mantidimaging.core.operations.rescale.rescale_test) test_type_changes_to_given_type() (in module mantidimaging.core.operations.rescale.rescale_test) to_partial() (mantidimaging.core.operation_history.operations.ImageOperation method) TomopyRecon (class in mantidimaging.core.reconstruct.tomopy_recon)

V

v_middle (mantidimaging.core.data.images.Images property) validate() (mantidimaging.core.operations.median_filter.median_filter.KernelSpinBox method) validate_execute_kwargs() (mantidimaging.core.operations.base_filter.BaseFilter static method) (mantidimaging.core.operations.divide.divide.DivideFilter static method) (mantidimaging.core.operations.flat_fielding.flat_fielding.FlatFieldFilter static method) (mantidimaging.core.operations.monitor_normalisation.monitor_normalisation.MonitorNormalisation static method) (mantidimaging.core.operations.rescale.rescale.RescaleFilter static method)

vec_geom_init2d() (in module mantidimaging.core.reconstruct.astra_recon)

W

wavelet_names() (in module mantidimaging.core.operations.remove_stripe.stripe_removal) WelcomeWindowTest (class in mantidimaging.eyes_tests.test_welcome_window) width (mantidimaging.core.data.images.Images property)

write_fits() (in module mantidimaging.core.io.saver) write_img() (in module mantidimaging.core.io.saver) write_nxs() (in module mantidimaging.core.io.saver)