Index

A

api() (in module xrf_explorer.server.routes.general)

apply_perspective_transformation() (in module xrf_explorer.server.image_register.register_image) apply_umap() (in module xrf_explorer.server.dim_reduction.embedding)

B

bin_data() (in module xrf_explorer.server.file_system.cubes.spectral) bin_raw_data() (in module xrf_explorer.server.routes.spectral_cube)

BITMASK_PATH (TestColorSegmentation attribute) BW_IMAGE_PATH (TestColorSegmentation attribute)

C

calculate_color_difference() (in module xrf_explorer.server.color_segmentation.color_seg) catch_all() (in module xrf_explorer) combine_bitmasks() (in module xrf_explorer.server.color_segmentation.color_seg) compute_fitting_dimensions_by_aspect() (in module xrf_explorer.server.image_register.register_image) compute_selection_mask() (in module xrf_explorer.server.image_to_cube_selection.image_to_cube_selection) CONFIG_PATH (TestImageRegistration attribute) contextual_image() (in module xrf_explorer.server.routes.images) contextual_image_recipe() (in module xrf_explorer.server.routes.images) contextual_image_size() (in module xrf_explorer.server.routes.images) convert_elemental_cube() (in module xrf_explorer.server.routes.elemental_cube) convert_elemental_cube_to_dms() (in module xrf_explorer.server.file_system.cubes.elemental) convert_to_hex() (in module xrf_explorer.server.color_segmentation.color_seg) convexHull() (in module xrf_explorer.server.image_to_cube_selection.image_to_cube_selection) create_data_source_dir() (in module xrf_explorer.server.routes.project) create_element_overlay() (in module xrf_explorer.server.dim_reduction.overlay) create_embedding_image() (in module xrf_explorer.server.dim_reduction.overlay)

create_image_of_indices_to_embedding() (in module xrf_explorer.server.dim_reduction.general) create_image_overlay() (in module xrf_explorer.server.dim_reduction.overlay) CubeType (class in xrf_explorer.server.image_to_cube_selection.image_to_cube_selection) CUSTOM_CONFIG_PATH (TestColorSegmentation attribute) (TestContextualImages attribute) (TestDimReduction attribute) (TestElementalData attribute) (TestImageToCubeSelection attribute) (TestSpectra attribute) (TestSpectral attribute) (TestUploadFileToServer attribute) (TestWorkspaceHandler attribute) CUSTOM_CONFIG_PATH_EMBEDDING_PRESENT (TestDimReduction attribute) CUSTOM_CONFIG_PATH_NO_EMBEDDING (TestDimReduction attribute) CUSTOM_CONFIG_PATH_NO_SOURCES (TestUploadFileToServer attribute) CUSTOM_DATA_FOLDER (TestWorkspaceHandler attribute) cvtColor() (in module xrf_explorer.server.dim_reduction.overlay)

D

DATA_CUBE_CSV (TestElementalData attribute) DATA_CUBE_DMS (TestElementalData attribute) DATA_CUBE_PATH (TestColorSegmentation attribute) data_cube_recipe() (in module xrf_explorer.server.routes.elemental_cube) data_cube_size() (in module xrf_explorer.server.routes.elemental_cube) DATA_SOURCE (TestColorSegmentation attribute) (TestImageRegistration attribute) DATA_SOURCE_FOLDER_NAME (TestImageToCubeSelection attribute) (TestSpectra attribute) (TestSpectral attribute) data_source_name_from_cube_path() (in module xrf_explorer.server.file_system.helper)

datasource_files() (in module xrf_explorer.server.routes.project) DATASOURCE_NAME (TestWorkspaceHandler attribute) DATASOURCE_NAME_NO_WORKSPACE (TestWorkspaceHandler attribute) delete_data_source() (in module xrf_explorer.server.routes.project) deregister_coord() (in module xrf_explorer.server.image_to_cube_selection.image_to_cube_selection) do_test_embedding() (TestDimReduction method) do_test_get_element_names() (TestElementalData method) do_test_get_elemental_cube() (TestElementalData method) do_test_get_elemental_map() (TestElementalData method) do_test_invalid_embedding_image() (TestDimReduction method) do_test_valid_image() (TestDimReduction method)

E

elem_threshold (TestColorSegmentation attribute) Elemental (CubeType attribute) ELEMENTAL_CUBE_NAME (TestWorkspaceHandler attribute) elemental_map() (in module xrf_explorer.server.routes.elemental_cube)

ElementLines (class in xrf_explorer.server.spectra.spectra) ELEMENTS (TestElementalData attribute) empty_array() (in module tests.color_segmentation.test_color_seg) EMPTY_SOURCE_NAME (TestSpectral attribute) encode_selection() (in module xrf_explorer.server.routes.helper)

F

fillPoly() (in module xrf_explorer.server.image_to_cube_selection.image_to_cube_selection)

filter_elemental_cube() (in module xrf_explorer.server.dim_reduction.embedding)

G

gaussian_convolve() (in module xrf_explorer.server.spectra.spectra) generate_embedding() (in module xrf_explorer.server.dim_reduction.embedding) get_average_data() (in module xrf_explorer.server.routes.spectral_cube) get_average_global() (in module xrf_explorer.server.spectra.spectra) get_average_selection() (in module xrf_explorer.server.spectra.spectra) get_base_image_name() (in module xrf_explorer.server.file_system.workspace.contextual_images) (in module xrf_explorer.server.file_system.workspace.file_access) get_base_image_path() (in module xrf_explorer.server.file_system.workspace.file_access) get_clusters_using_k_means() (in module xrf_explorer.server.color_segmentation.color_seg) get_color_cluster_bitmask() (in module xrf_explorer.server.routes.color_segmentation) get_color_clusters() (in module xrf_explorer.server.routes.color_segmentation) get_config() (in module xrf_explorer.server.file_system.helper) get_contextual_image() (in module xrf_explorer.server.file_system.workspace.contextual_images) get_contextual_image_data() (in module xrf_explorer.server.file_system.workspace.contextual_images) get_contextual_image_path() (in module xrf_explorer.server.file_system.workspace.contextual_images) get_contextual_image_recipe_path() (in module xrf_explorer.server.file_system.workspace.contextual_images) get_contextual_image_size() (in module xrf_explorer.server.file_system.workspace.contextual_images) get_data_source_files() (in module xrf_explorer.server.file_system.sources.data_listing) get_data_sources_names() (in module xrf_explorer.server.file_system.sources.data_listing) get_dr_embedding() (in module xrf_explorer.server.routes.dim_reduction) get_dr_embedding_mapping() (in module xrf_explorer.server.routes.dim_reduction) get_dr_overlay() (in module xrf_explorer.server.routes.dim_reduction) get_element_averages() (in module xrf_explorer.server.file_system.cubes.elemental) get_element_averages_selection() (in module xrf_explorer.server.file_system.cubes.elemental) get_element_names() (in module xrf_explorer.server.file_system.cubes.elemental) get_element_spectra() (in module xrf_explorer.server.routes.spectral_cube) get_element_spectrum() (in module xrf_explorer.server.spectra.spectra) get_elemental_clusters_using_k_means() (in module xrf_explorer.server.color_segmentation.color_seg) get_elemental_cube_file_names() (in module xrf_explorer.server.file_system.workspace.file_access) get_elemental_cube_path() (in module xrf_explorer.server.file_system.workspace.file_access) get_elemental_cube_path_from_name() (in module xrf_explorer.server.file_system.workspace.file_access) get_elemental_cube_recipe_path() (in module xrf_explorer.server.file_system.workspace.file_access)

get_elemental_data_cube() (in module xrf_explorer.server.file_system.cubes.elemental) get_elemental_data_cube_from_csv() (in module xrf_explorer.server.file_system.cubes.convert_csv) get_elemental_data_cube_from_dms() (in module xrf_explorer.server.file_system.cubes.convert_dms) get_elemental_datacube_dimensions() (in module xrf_explorer.server.file_system.cubes.convert_dms) get_elemental_map() (in module xrf_explorer.server.file_system.cubes.elemental) get_elemental_map_from_csv() (in module xrf_explorer.server.file_system.cubes.convert_csv) get_elemental_map_from_dms() (in module xrf_explorer.server.file_system.cubes.convert_dms) get_elements_from_csv() (in module xrf_explorer.server.file_system.cubes.convert_csv) get_elements_from_dms() (in module xrf_explorer.server.file_system.cubes.convert_dms) get_filestorage_object() (TestUploadFileToServer static method) get_image_of_indices_to_embedding() (in module xrf_explorer.server.dim_reduction.general) get_image_registered_to_data_cube() (in module xrf_explorer.server.image_register.register_image) get_offset() (in module xrf_explorer.server.routes.spectral_cube) get_path_to_base_image() (in module xrf_explorer.server.file_system.workspace.contextual_images) get_path_to_cs_folder() (in module xrf_explorer.server.color_segmentation.helper) get_path_to_dr_folder() (in module xrf_explorer.server.dim_reduction.general) get_path_to_generated_folder() (in module xrf_explorer.server.file_system.helper) get_path_to_workspace() (in module xrf_explorer.server.file_system.workspace.workspace_handler) get_raw_data() (in module xrf_explorer.server.file_system.cubes.spectral) get_raw_rpl_names() (in module xrf_explorer.server.file_system.workspace.file_access) get_raw_rpl_paths() (in module xrf_explorer.server.file_system.workspace.file_access) get_scaled_cube_coordinates() (in module xrf_explorer.server.image_to_cube_selection.image_to_cube_selection) get_selection() (in module xrf_explorer.server.image_to_cube_selection.image_to_cube_selection) get_selection_spectra() (in module xrf_explorer.server.routes.spectral_cube) get_short_element_names() (in module xrf_explorer.server.file_system.cubes.elemental) get_spectra_params() (in module xrf_explorer.server.file_system.cubes.spectral) get_spectral_cube_recipe_path() (in module xrf_explorer.server.file_system.workspace.file_access) get_theoretical_data() (in module xrf_explorer.server.spectra.spectra) get_workspace() (in module xrf_explorer.server.routes.project) get_workspace_dict() (in module xrf_explorer.server.file_system.workspace.file_access) getPerspectiveTransform() (in module xrf_explorer.server.image_register.register_image) (in module xrf_explorer.server.image_to_cube_selection.image_to_cube_selection)

I

IMAGE_NAME (TestColorSegmentation attribute) (TestImageRegistration attribute) image_to_lab() (in module xrf_explorer.server.color_segmentation.color_seg) image_to_rgb() (in module xrf_explorer.server.color_segmentation.color_seg) imread() (in module tests.test_image_to_cube_selection) (in module xrf_explorer.server.image_register.register_image) (in module xrf_explorer.server.image_to_cube_selection.image_to_cube_selection)

imwrite() (in module xrf_explorer.server.dim_reduction.general) (in module xrf_explorer.server.image_register.register_image) INVALID_IMAGE_PATH (TestContextualImages attribute) inverse_register_image() (in module xrf_explorer.server.image_register.register_image) is_base_image() (in module xrf_explorer.server.file_system.workspace.contextual_images) is_deregistration_correct() (TestImageToCubeSelection method)

K

k (TestColorSegmentation attribute)

L

lab_to_rgb() (in module xrf_explorer.server.color_segmentation.color_seg) list_accessible_data_sources() (in module xrf_explorer.server.routes.project) list_element_averages() (in module xrf_explorer.server.routes.elemental_cube) list_element_averages_selection() (in module xrf_explorer.server.routes.elemental_cube)

list_element_names() (in module xrf_explorer.server.routes.elemental_cube) load_image_to_register() (in module xrf_explorer.server.image_register.register_image) load_points() (in module xrf_explorer.server.image_register.register_image) load_points_dict() (in module xrf_explorer.server.image_register.register_image)

M

merge_similar_colors() (in module xrf_explorer.server.color_segmentation.color_seg) mipmap_exists() (in module xrf_explorer.server.file_system.cubes.spectral) mipmap_raw_cube() (in module xrf_explorer.server.file_system.cubes.spectral) module run tests tests.color_segmentation tests.color_segmentation.manual_testing_color_seg tests.color_segmentation.test_color_seg tests.file_system tests.file_system.test_element_data tests.file_system.test_file_upload tests.file_system.test_spectral tests.file_system.test_workspace_handler tests.test_contextual_images tests.test_dim_reduction tests.test_image_registration tests.test_image_to_cube_selection tests.test_spectra xrf_explorer xrf_explorer.server xrf_explorer.server.color_segmentation xrf_explorer.server.color_segmentation.color_seg xrf_explorer.server.color_segmentation.helper xrf_explorer.server.dim_reduction xrf_explorer.server.dim_reduction.embedding xrf_explorer.server.dim_reduction.general xrf_explorer.server.dim_reduction.overlay xrf_explorer.server.file_system xrf_explorer.server.file_system.cubes xrf_explorer.server.file_system.cubes.convert_csv xrf_explorer.server.file_system.cubes.convert_dms xrf_explorer.server.file_system.cubes.elemental xrf_explorer.server.file_system.cubes.spectral xrf_explorer.server.file_system.helper xrf_explorer.server.file_system.sources xrf_explorer.server.file_system.sources.data_listing xrf_explorer.server.file_system.workspace xrf_explorer.server.file_system.workspace.contextual_images xrf_explorer.server.file_system.workspace.file_access xrf_explorer.server.file_system.workspace.workspace_handler xrf_explorer.server.image_register xrf_explorer.server.image_register.register_image xrf_explorer.server.image_to_cube_selection xrf_explorer.server.image_to_cube_selection.image_to_cube_selection xrf_explorer.server.routes xrf_explorer.server.routes.color_segmentation xrf_explorer.server.routes.dim_reduction xrf_explorer.server.routes.elemental_cube xrf_explorer.server.routes.general xrf_explorer.server.routes.helper xrf_explorer.server.routes.images xrf_explorer.server.routes.project xrf_explorer.server.routes.spectral_cube xrf_explorer.server.spectra xrf_explorer.server.spectra.spectra

N

NAME_CUBE_FROM_CSV (TestElementalData attribute) NO_CUBE_DATA_SOURCE (TestDimReduction attribute) NO_OFFSET_NAME (TestSpectral attribute) NO_RAW_SOURCE_NAME (TestSpectral attribute) NO_WORKSPACE_NAME (TestSpectral attribute)

NON_EXISTING_CUBE (TestElementalData attribute) NONEXISTENT_IMAGE_PATH (TestContextualImages attribute) normalize_elemental_cube_per_layer() (in module xrf_explorer.server.file_system.cubes.elemental) normalize_ndarray_to_grayscale() (in module xrf_explorer.server.file_system.cubes.elemental) num_attempts (TestColorSegmentation attribute) numpy_to_raw() (TestSpectral method)

P

pad_image_to_match_size() (in module xrf_explorer.server.image_register.register_image) parse_rpl() (in module xrf_explorer.server.file_system.cubes.spectral) parse_selection() (in module xrf_explorer.server.routes.helper) PATH_CONTROL_POINTS (TestImageRegistration attribute) PATH_CUBE (TestImageRegistration attribute) PATH_DATA_SOURCE (TestColorSegmentation attribute) PATH_GENERATED_FOLDER (TestDimReduction attribute) PATH_IMAGE_REFERENCE (TestImageRegistration attribute)

PATH_IMAGE_REGISTER (TestImageRegistration attribute) PATH_RESULT (TestImageRegistration attribute) PATH_TEST_CUBE (TestDimReduction attribute) PATH_TO_TEST_FOLDER (TestElementalData attribute) perspective_transform_coord() (in module xrf_explorer.server.image_to_cube_selection.image_to_cube_selection) perspectiveTransform() (in module xrf_explorer.server.image_to_cube_selection.image_to_cube_selection) plot_embedding_with_overlay() (in module xrf_explorer.server.dim_reduction.overlay) Polygon (SelectionType attribute)

R

Raw (CubeType attribute) RAW_ELEMENTAL_CUBE (TestElementalData attribute) Rectangle (SelectionType attribute) REG_TEST_IMAGE_PATH (TestColorSegmentation attribute) register_image() (in module xrf_explorer.server.image_register.register_image) register_image_to_image() (in module xrf_explorer.server.image_register.register_image) remove_data_source() (in module xrf_explorer.server.routes.project) reshape_image() (in module xrf_explorer.server.color_segmentation.color_seg)

resize() (in module xrf_explorer.server.image_register.register_image) resize_image_fit_aspect_ratio() (in module xrf_explorer.server.image_register.register_image) RESOURCES_PATH (TestContextualImages attribute) (TestSpectra attribute) (TestSpectral attribute) rgb_to_hex() (in module xrf_explorer.server.color_segmentation.color_seg) rgb_to_lab() (in module xrf_explorer.server.color_segmentation.color_seg) run module

S

SAMPLE_BASE_IMAGE_PATH (TestImageToCubeSelection attribute) SAMPLE_CUBE_IMG_PATH (TestImageToCubeSelection attribute) SAMPLE_CUBE_RECIPE_PATH (TestImageToCubeSelection attribute) save_bitmask_as_png() (in module xrf_explorer.server.color_segmentation.color_seg) SelectionType (class in xrf_explorer.server.image_to_cube_selection.image_to_cube_selection) set_binned() (in module xrf_explorer.server.file_system.workspace.file_access) set_config() (in module xrf_explorer.server.file_system.helper)

setup_environment() (TestElementalData method) (TestImageRegistration method) (TestImageToCubeSelection method) (TestSpectra method) (TestSpectral method) setup_get_elemental_clusters() (TestColorSegmentation method) SOURCE_FOLDER_CSV (TestElementalData attribute) SOURCE_FOLDER_DMS (TestElementalData attribute)

T

test_bin_data_() (TestSpectral method) test_bin_data_default_params() (TestSpectral method) test_bin_data_empty_rpl() (TestSpectral method) test_bin_data_identity() (TestSpectral method) test_bin_data_no_raw() (TestSpectral method) test_bin_data_wrong_size() (TestSpectral method) test_combined_bitmasks() (TestColorSegmentation method) test_combined_empty_bitmasks() (TestColorSegmentation method) test_config_not_found() (TestDimReduction method) test_config_not_found_get_workspace() (TestWorkspaceHandler method) test_config_not_found_update_workspace() (TestWorkspaceHandler method) test_convert_to_hex() (TestColorSegmentation method) test_csv_to_dms() (TestElementalData method) test_csv_to_dms_directly() (TestElementalData method) TEST_DATA_SOURCE (TestDimReduction attribute) test_datasource_not_found_get_workspace() (TestWorkspaceHandler method) test_datasource_not_found_update_workspace() (TestWorkspaceHandler method) test_deregister_coord() (TestImageToCubeSelection method) test_get_average_global() (TestSpectra method) test_get_average_selection() (TestSpectra method) test_get_average_selection_config_none() (TestSpectra method) test_get_base_image_name() (TestWorkspaceHandler method) test_get_base_image_name_no_config() (TestWorkspaceHandler method) test_get_base_image_name_no_workspace() (TestWorkspaceHandler method) test_get_base_image_path_no_config() (TestWorkspaceHandler method) test_get_base_image_path_no_filepath() (TestWorkspaceHandler method) test_get_clusters_using_k_means_colors() (TestColorSegmentation method) test_get_clusters_using_k_means_colors_register_fail() (TestColorSegmentation method) test_get_contextual_image_image() (TestContextualImages method) test_get_contextual_image_image_invalid() (TestContextualImages method) test_get_contextual_image_image_nonexistent() (TestContextualImages method) test_get_contextual_image_invalid_size() (TestContextualImages method) test_get_contextual_image_nonexistent_size() (TestContextualImages method) test_get_contextual_image_path_base() (TestContextualImages method) test_get_contextual_image_path_contextual() (TestContextualImages method) test_get_contextual_image_path_invalid_config() (TestContextualImages method) test_get_contextual_image_path_invalid_painting() (TestContextualImages method) test_get_contextual_image_path_nonexistent() (TestContextualImages method) test_get_contextual_image_recipe_path_base() (TestContextualImages method) test_get_contextual_image_recipe_path_contextual() (TestContextualImages method) test_get_contextual_image_recipe_path_nonexistent() (TestContextualImages method) test_get_contextual_image_size() (TestContextualImages method) test_get_cube_coordinates() (TestImageToCubeSelection method) test_get_data_source_files() (TestUploadFileToServer method) test_get_data_source_files_invalid_config() (TestUploadFileToServer method) test_get_data_source_files_invalid_path() (TestUploadFileToServer method) test_get_data_source_names_invalid_config() (TestUploadFileToServer method) test_get_elem_clusters_using_k_means() (TestColorSegmentation method) test_get_elem_clusters_using_k_means_elemental_not_found() (TestColorSegmentation method) test_get_elem_clusters_using_k_means_empty_mask() (TestColorSegmentation method) test_get_elem_clusters_using_k_means_register_fail() (TestColorSegmentation method) test_get_element_averages() (TestElementalData method) test_get_element_averages_invalid_data_source() (TestElementalData method) test_get_element_averages_selection() (TestElementalData method) test_get_element_names() (TestElementalData method) test_get_element_names_invalid_data_source() (TestElementalData method) test_get_elemental_cube() (TestElementalData method) test_get_elemental_cube_path_from_name_invalid_name() (TestWorkspaceHandler method) test_get_elemental_cube_path_from_name_no_config() (TestWorkspaceHandler method) test_get_elemental_cube_path_from_name_no_workspace() (TestWorkspaceHandler method) test_get_elemental_map() (TestElementalData method) test_get_elemental_map_invalid_type() (TestElementalData method) test_get_file_names() (TestUploadFileToServer method) test_get_get_workspace_dict_no_config() (TestWorkspaceHandler method) test_get_path_to_base_image() (TestContextualImages method) test_get_path_to_cs_folder() (TestColorSegmentation method) test_get_path_to_cs_folder_wrong_datasource() (TestColorSegmentation method) test_get_raw_data() (TestSpectra method) test_get_selected_data_cube_dir_found() (TestImageToCubeSelection method) test_get_selected_data_cube_dir_not_found() (TestImageToCubeSelection method) test_get_selected_data_cube_invalid_cubetype() (TestImageToCubeSelection method) test_get_selected_data_cube_invalid_polygon() (TestImageToCubeSelection method) test_get_selected_data_cube_invalid_rectangle() (TestImageToCubeSelection method) test_get_selected_data_cube_output_size() (TestImageToCubeSelection method) test_get_short_element_names_invalid_data_source() (TestElementalData method) test_get_spectra_params() (TestSpectral method) test_get_spectra_params_file_not_found() (TestSpectral method) test_get_spectral_cube_recipe_path_no_config() (TestWorkspaceHandler method) test_get_spectral_cube_recipe_path_no_workspace() (TestWorkspaceHandler method) test_get_theoretical_data() (TestSpectra method) test_get_theoretical_data_invalid_element() (TestSpectra method) test_high_threshold() (TestDimReduction method) TEST_IMAGE_PATH (TestColorSegmentation attribute) (TestContextualImages attribute) test_image_to_rgb_and_lab() (TestColorSegmentation method) test_invalid_contextual_image_type() (TestDimReduction method) test_invalid_create_image_of_indices_invalid_data_source() (TestDimReduction method) test_invalid_create_image_of_indices_no_cube() (TestDimReduction method) test_invalid_create_image_of_indices_no_files() (TestDimReduction method) test_invalid_element_creating_image() (TestDimReduction method)

test_invalid_element_generating() (TestDimReduction method) test_invalid_getting_image_of_indices_invalid_data_source() (TestDimReduction method) test_invalid_getting_image_of_indices_no_image() (TestDimReduction method) test_invalid_image_type() (TestDimReduction method) test_invalid_umap() (TestDimReduction method) test_merge_similar_colors() (TestColorSegmentation method) test_merge_similar_colors_empty() (TestColorSegmentation method) test_mipmap_create() (TestSpectra method) test_mipmap_data() (TestSpectra method) test_mipmap_inexistent_data_source() (TestSpectra method) test_mipmap_low_level() (TestSpectra method) test_mipmap_not_exist() (TestSpectra method) test_nan_embedding() (TestDimReduction method) test_negative_coordinates() (TestImageToCubeSelection method) test_no_cube_for_embedding() (TestDimReduction method) test_no_embedding() (TestDimReduction method) test_no_file_names() (TestUploadFileToServer method) test_parse_rpl() (TestSpectral method) test_parse_rpl_empty_file() (TestSpectral method) test_parse_rpl_file_not_found() (TestSpectral method) TEST_RAW_DATA (TestSpectra attribute) TEST_RAW_PATH (TestSpectra attribute) (TestSpectral attribute) TEST_RECIPE_PATH (TestContextualImages attribute) test_register_image_to_cube_data_cube_not_found() (TestImageRegistration method) test_register_image_to_cube_image_register_not_found() (TestImageRegistration method) test_register_image_to_cube_success() (TestImageRegistration method) test_register_image_to_image_csv_not_found() (TestImageRegistration method) test_register_image_to_image_destination_not_found() (TestImageRegistration method) test_register_image_to_image_reference_not_found() (TestImageRegistration method) test_register_image_to_image_register_not_found() (TestImageRegistration method) test_register_image_to_image_success() (TestImageRegistration method) test_rgb_to_lab() (TestColorSegmentation method) test_ribbon_selection() (TestImageToCubeSelection method) test_save_bitmask() (TestColorSegmentation method) test_save_bitmask_invalid_bitmask() (TestColorSegmentation method) test_save_bitmask_wrong_path() (TestColorSegmentation method) test_selection_raw_cube() (TestImageToCubeSelection method) test_selections_equivalent() (TestImageToCubeSelection method) test_to_dms_cube_name_includes_file_extension() (TestElementalData method) test_to_dms_invalid_folder_path() (TestElementalData method) test_update_bin_params() (TestSpectral method) test_update_bin_params_default() (TestSpectral method) test_update_bin_params_no_offset() (TestSpectral method) test_update_workspace() (TestWorkspaceHandler method) test_valid_contextual_image() (TestDimReduction method) test_valid_create_embedding_image() (TestDimReduction method) test_valid_elemental_image() (TestDimReduction method) test_valid_embedding() (TestDimReduction method) test_valid_embedding_downsampled() (TestDimReduction method) test_workspace_found() (TestWorkspaceHandler method) TestColorSegmentation (class in tests.color_segmentation.test_color_seg) TestContextualImages (class in tests.test_contextual_images) TestDimReduction (class in tests.test_dim_reduction) TestElementalData (class in tests.file_system.test_element_data) TestImageRegistration (class in tests.test_image_registration) TestImageToCubeSelection (class in tests.test_image_to_cube_selection) tests module tests.color_segmentation module tests.color_segmentation.manual_testing_color_seg module tests.color_segmentation.test_color_seg module tests.file_system module tests.file_system.test_element_data module tests.file_system.test_file_upload module tests.file_system.test_spectral module tests.file_system.test_workspace_handler module tests.test_contextual_images module tests.test_dim_reduction module tests.test_image_registration module tests.test_image_to_cube_selection module tests.test_spectra module TestSpectra (class in tests.test_spectra) TestSpectral (class in tests.file_system.test_spectral) TestUploadFileToServer (class in tests.file_system.test_file_upload) TestWorkspaceHandler (class in tests.file_system.test_workspace_handler) to_dms() (in module xrf_explorer.server.file_system.cubes.convert_dms)

U

update_bin_params() (in module xrf_explorer.server.file_system.cubes.spectral) update_workspace() (in module xrf_explorer.server.file_system.workspace.workspace_handler)

upload_chunk() (in module xrf_explorer.server.routes.project) UPLOAD_FILE_PATH (TestUploadFileToServer attribute)

V

valid_element() (in module xrf_explorer.server.dim_reduction.general)

validate_config() (in module xrf_explorer.server.routes.helper) visualize_clusters() (in module tests.color_segmentation.manual_testing_color_seg)

W

warpPerspective() (in module xrf_explorer.server.image_register.register_image) WORKSPACE_BASE_IMAGE_PATH (TestImageToCubeSelection attribute)

WRONG_CONFIG_PATH (TestColorSegmentation attribute) WRONG_SIZE_NAME (TestSpectral attribute)

X

xrf_explorer module xrf_explorer.server module xrf_explorer.server.color_segmentation module xrf_explorer.server.color_segmentation.color_seg module xrf_explorer.server.color_segmentation.helper module xrf_explorer.server.dim_reduction module xrf_explorer.server.dim_reduction.embedding module xrf_explorer.server.dim_reduction.general module xrf_explorer.server.dim_reduction.overlay module xrf_explorer.server.file_system module xrf_explorer.server.file_system.cubes module xrf_explorer.server.file_system.cubes.convert_csv module xrf_explorer.server.file_system.cubes.convert_dms module xrf_explorer.server.file_system.cubes.elemental module xrf_explorer.server.file_system.cubes.spectral module xrf_explorer.server.file_system.helper module xrf_explorer.server.file_system.sources module xrf_explorer.server.file_system.sources.data_listing module xrf_explorer.server.file_system.workspace module

xrf_explorer.server.file_system.workspace.contextual_images module xrf_explorer.server.file_system.workspace.file_access module xrf_explorer.server.file_system.workspace.workspace_handler module xrf_explorer.server.image_register module xrf_explorer.server.image_register.register_image module xrf_explorer.server.image_to_cube_selection module xrf_explorer.server.image_to_cube_selection.image_to_cube_selection module xrf_explorer.server.routes module xrf_explorer.server.routes.color_segmentation module xrf_explorer.server.routes.dim_reduction module xrf_explorer.server.routes.elemental_cube module xrf_explorer.server.routes.general module xrf_explorer.server.routes.helper module xrf_explorer.server.routes.images module xrf_explorer.server.routes.project module xrf_explorer.server.routes.spectral_cube module xrf_explorer.server.spectra module xrf_explorer.server.spectra.spectra module