Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y A A0 (coseda.ici.step1_hillmap_wrmsd.Step1Params attribute) abort() (cosedaUI.strip_file_window.StripWorker method) (cosedaUI.strip_file_window.StripWorkerBatch method) abort_stripping() (cosedaUI.strip_file_window.StripFilesWindow method) AboutWindow (class in cosedaUI.about_window) add_emd_file() (cosedaUI.importers.import_emd_window.ImportEMDWindow method) (cosedaUI.importers.ImportEMDWindow method) add_emd_folder() (cosedaUI.importers.import_emd_window.ImportEMDWindow method) (cosedaUI.importers.ImportEMDWindow method) add_generated_ini_paths() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.workspace.WorkspaceMixin method) (cosedaUI.mainwindow_sections.WorkspaceMixin method) (in module cosedaUI.workspace_functions) add_h5_files() (cosedaUI.ici_window.OrchestratorWidget method) add_ini_files() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.workspace.WorkspaceMixin method) (cosedaUI.mainwindow_sections.WorkspaceMixin method) (in module cosedaUI.workspace_functions) add_ini_paths() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.workspace.WorkspaceMixin method) (cosedaUI.mainwindow_sections.WorkspaceMixin method) (in module cosedaUI.workspace_functions) add_intesities_batch() (in module coseda.importers.import_velox) add_mrc_file() (cosedaUI.importers.import_mrc_window.ImportMRCWindow method) (cosedaUI.importers.ImportMRCWindow method) add_mrc_folder() (cosedaUI.importers.import_mrc_window.ImportMRCWindow method) (cosedaUI.importers.ImportMRCWindow method) add_note() (coseda.centerrefinement.cancellation.RefinementCancelled method) add_plot_to_viewer() (cosedaUI.findcenters_window.CenterFinderSettingsWindow method) (cosedaUI.refinecenters_window.CenterRefinementSettingsWindow method) add_scalebar() (in module coseda.map.streaks) adjust_brightness() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.viewer.ViewerMixin method) (cosedaUI.mainwindow_sections.ViewerMixin method) adjust_brightness_value() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.viewer.ViewerMixin method) (cosedaUI.mainwindow_sections.ViewerMixin method) adjust_contrast() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.viewer.ViewerMixin method) (cosedaUI.mainwindow_sections.ViewerMixin method) adjust_contrast_value() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.viewer.ViewerMixin method) (cosedaUI.mainwindow_sections.ViewerMixin method) adjust_gamma() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.viewer.ViewerMixin method) (cosedaUI.mainwindow_sections.ViewerMixin method) adjust_gamma_value() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.viewer.ViewerMixin method) (cosedaUI.mainwindow_sections.ViewerMixin method) all_next_done_for_latest() (in module coseda.ici.orchestrator) allow_spacing_relax (coseda.ici.step1_hillmap_wrmsd.Step1Params attribute) append_text() (cosedaUI.ici_window.OrchestratorWidget method) apply_center_finder_settings() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.workspace.WorkspaceMixin method) (cosedaUI.mainwindow_sections.WorkspaceMixin method) apply_peakfinder_settings() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.workspace.WorkspaceMixin method) (cosedaUI.mainwindow_sections.WorkspaceMixin method) apply_settings() (cosedaUI.peakfinder_window.PeakFinderSettingsWindow method) apply_to_workspace() (cosedaUI.metadata_window.MetadataWindow method) are_touching() (in module coseda.map.mapping) args (coseda.centerrefinement.cancellation.RefinementCancelled attribute) AspectRatioWidget (class in cosedaUI.mainwindow) assign_streaks() (in module coseda.map.streaks) aurora_points_cache_path() (in module coseda.peakfinding.aurora) AuroraPlotWindow (class in cosedaUI.aurora_window) AuroraPlotWorker (class in cosedaUI.aurora_window) auto_display_initial() (cosedaUI.findcenters_window.PreviewWindow method) B bin_chunk() (in module coseda.importers.convert_dm4) (in module coseda.importers.h5convert) browse_cell() (cosedaUI.ici_window.OrchestratorWidget method) browse_dest() (cosedaUI.importers.import_h5_window.ImportH5Window method) (cosedaUI.importers.ImportH5Window method) browse_file() (cosedaUI.importers.import_h5_window.ImportH5Window method) (cosedaUI.importers.ImportH5Window method) browse_geom() (cosedaUI.ici_window.OrchestratorWidget method) browse_run_root() (cosedaUI.ici_window.OrchestratorWidget method) build_argparser() (in module coseda.ici.no_run_prep_singlelist) build_argv() (cosedaUI.ici_window.OrchestratorWidget method) build_geomfile_from_ini() (in module coseda.geomfile) build_plans_from_state() (in module coseda.ici.build_early_break_from_log) build_stream_for_plans() (in module coseda.ici.build_early_break_from_log) C calculate() (cosedaUI.metadata_window.PixelCalcDialog method) calculate_electron_wavelength() (in module cosedaUI.geomfile_window) calculate_mean_intensities() (in module coseda.importers.import_velox) calculate_mean_intensities_batch() (in module coseda.pipeline.frame_intensities) calculate_mean_intensities_chunked() (in module coseda.importers.import_velox) calculate_mean_intensities_dask_batch() (in module coseda.pipeline) (in module coseda.pipeline.frame_intensities) calculate_mean_intensities_dask_file() (in module coseda.pipeline) (in module coseda.pipeline.frame_intensities) calculate_mean_intensities_dask_file_inprocess() (in module coseda.pipeline) (in module coseda.pipeline.frame_intensities) calculate_mean_intensity_per_frame_batch() (in module coseda.importers.h5convert) calculate_radial_profiles() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.workspace.WorkspaceMixin method) (cosedaUI.mainwindow_sections.WorkspaceMixin method) calculate_radial_profiles_batch() (in module coseda.pipeline.frame_intensities) calculate_radial_profiles_dask_file() (in module coseda.pipeline.frame_intensities) calculate_radial_profiles_dask_file_inprocess() (in module coseda.pipeline.frame_intensities) calculate_total_intensities() (in module coseda.importers.import_velox) calculate_total_intensities_chunked() (in module coseda.importers.import_velox) calculate_total_intensity_per_frame_batch() (in module coseda.importers.h5convert) cancelled (cosedaUI.findcenters_window.Worker attribute) (cosedaUI.refinecenters_window.Worker attribute) canonical_stream_filename() (in module coseda.ici.run_contract) canonical_stream_path() (in module coseda.ici.run_contract) cell_path (coseda.unitcell_fit.WorkspaceStreamSource attribute) CellfileMixin (class in cosedaUI.indexintegrate_sections) (class in cosedaUI.indexintegrate_sections.cellfile) CellfileWindow (class in cosedaUI.cellfile_window) CenterFinderSettingsWindow (class in cosedaUI.findcenters_window) CenterRefinementSettingsWindow (class in cosedaUI.refinecenters_window) change_frame() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.viewer.ViewerMixin method) (cosedaUI.mainwindow_sections.ViewerMixin method) change_frame_from_entry() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.viewer.ViewerMixin method) (cosedaUI.mainwindow_sections.ViewerMixin method) check_and_enable_findpeaks_button() (cosedaUI.peakfinder_window.PeakFinderSettingsWindow method) check_cancel() (in module coseda.centerrefinement.cancellation) check_disk_space() (in module coseda.pipeline.strip_h5) check_findcenters_allowed() (in module cosedaUI.workflow_wizzard) check_for_updates() (in module cosedaUI.update) check_if_index_dataset_exists() (in module coseda.pipeline.strip_h5) check_if_peaks_and_intensities_datasets_exist() (in module coseda.pipeline.strip_h5) check_if_stripped() (in module coseda.pipeline) (in module coseda.pipeline.strip_h5) check_image_dataset() (in module coseda.importers.import_h5) check_index_integrate_allowed() (in module cosedaUI.workflow_wizzard) check_peakfinding_allowed() (in module cosedaUI.workflow_wizzard) check_refinecenters_allowed() (in module cosedaUI.workflow_wizzard) chunk_key_from_slice() (in module coseda.ici.build_early_break_from_log) ChunkRow (class in coseda.ici.evaluate_stream) clear_h5_files() (cosedaUI.ici_window.OrchestratorWidget method) clear_vdf_overlay() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.viewer.ViewerMixin method) (cosedaUI.mainwindow_sections.ViewerMixin method) ClickableLabel (class in cosedaUI.refinecenters_window) close_client() (coseda.dask_client_manager.DaskClientManager class method) closeEvent() (cosedaUI.aurora_window.AuroraPlotWindow method) (cosedaUI.findcenters_window.CenterFinderSettingsWindow method) (cosedaUI.ici_window.OrchestratorMainWindow method) (cosedaUI.importers.import_emd_window.ImportEMDWindow method) (cosedaUI.importers.ImportEMDWindow method) (cosedaUI.map_window.MapWindow method) (cosedaUI.peakfinder_window.PeakFinderSettingsWindow method) (cosedaUI.refinecenters_window.CenterRefinementSettingsWindow method) (cosedaUI.unitcell_window.UnitCellHistogramWindow method) cluster_segments() (in module coseda.map.mapping) ClusterMixin (class in cosedaUI.mainwindow_sections) (class in cosedaUI.mainwindow_sections.cluster) col_dx (coseda.ici.step2_dxdy.Step2DxDyConfig attribute) col_dy (coseda.ici.step2_dxdy.Step2DxDyConfig attribute) collect_latest_numeric_proposals() (in module coseda.ici.build_overlays_and_list) compare_peaks() (cosedaUI.indexing_stream_manager.IndexingStreamManager method) compare_strokes() (in module coseda.map.findscanlines) compute_aurora_histogram() (in module coseda.peakfinding.aurora) compute_aurora_histogram_for_files() (in module coseda.peakfinding.aurora) compute_aurora_points() (in module coseda.peakfinding.aurora) compute_auto_significance_threshold() (in module coseda.centerfinding.findcenters_direct) concat_streams() (in module coseda.ici.run_sh) config_to_paths() (in module coseda.initialize) (in module coseda.io) configure_logging() (in module coseda.logging_utils) confirm_metadata_edit() (cosedaUI.metadata_window.MetadataWindow method) corrected_to_raw() (in module coseda.detector_geometry) corrected_to_raw_points() (in module coseda.detector_geometry) coseda module coseda.centerfinding module coseda.centerfinding.findcenters_beamstop module coseda.centerfinding.findcenters_direct module coseda.centerrefinement module coseda.centerrefinement.cancellation module coseda.centerrefinement.refinecenters_beamstop module coseda.centerrefinement.refinecenters_direct module coseda.crystfel_cell module coseda.dask_client_manager module coseda.detector_geometry module coseda.export module coseda.exporters.hklf4 module coseda.geomfile module coseda.ici module coseda.ici.build_early_break_from_log module coseda.ici.build_overlays_and_list module coseda.ici.create_run_sh module coseda.ici.evaluate_stream module coseda.ici.extract_mille_shifts module coseda.ici.fix_stream_paths module coseda.ici.no_run_prep_singlelist module coseda.ici.orchestrator module coseda.ici.overlay_elink module coseda.ici.propose_next_shifts module coseda.ici.run_contract module coseda.ici.run_sh module coseda.ici.step1_hillmap_wrmsd module coseda.ici.step2_dxdy module coseda.ici.summarize_image_run_log module coseda.ici.update_image_run_log_grouped module coseda.importers module coseda.importers.convert_dm4 module coseda.importers.gatan_metareader module coseda.importers.h5convert module coseda.importers.import_h5 module coseda.importers.import_mrc module coseda.importers.import_tiff module coseda.importers.import_velox module coseda.indexintegrate module coseda.initialize module coseda.initialize.insfiles module coseda.initialize.project_files module coseda.initialize.settings module coseda.io module coseda.logging_utils module coseda.map module coseda.map.findscanlines module coseda.map.mapping module coseda.map.streaks module coseda.merge module coseda.nexus module coseda.nexus.detector module coseda.nexus.goniometer module coseda.nexus.groups module coseda.nexus.images module coseda.nexus.indices module coseda.nexus.logs module coseda.nexus.paths module coseda.nexus.peaks module coseda.nexus.process module coseda.peakfinding module coseda.peakfinding.aurora module coseda.peakfinding.findpeaks module coseda.peakfinding.findpeaks_dask module coseda.peakfinding.maxres module coseda.peakfinding.peakfinder9 module coseda.pipeline module coseda.pipeline.frame_intensities module coseda.pipeline.processimage module coseda.pipeline.strip_h5 module coseda.pixmask module coseda.unitcell_fit module cosedaUI module cosedaUI (class in cosedaUI.mainwindow) cosedaUI.about_window module cosedaUI.aurora_window module cosedaUI.cellfile_window module cosedaUI.export module cosedaUI.findcenters_window module cosedaUI.geomfile_window module cosedaUI.h5_metadata_loader module cosedaUI.ici_window module cosedaUI.image_tools module cosedaUI.importers module cosedaUI.importers.import_emd_window module cosedaUI.importers.import_h5_window module cosedaUI.importers.import_mrc_window module cosedaUI.importers.import_tiff_window module cosedaUI.indexing_stream_manager module cosedaUI.indexintegrate_sections module cosedaUI.indexintegrate_sections.cellfile module cosedaUI.indexintegrate_sections.geomfile module cosedaUI.indexintegrate_sections.helpers module cosedaUI.indexintegrate_sections.ici module cosedaUI.indexintegrate_sections.index_settings module cosedaUI.indexintegrate_sections.run_control module cosedaUI.indexintegrate_window module cosedaUI.mainwindow module cosedaUI.mainwindow_sections module cosedaUI.mainwindow_sections.cluster module cosedaUI.mainwindow_sections.imports module cosedaUI.mainwindow_sections.indexing module cosedaUI.mainwindow_sections.viewer module cosedaUI.mainwindow_sections.workflow module cosedaUI.mainwindow_sections.workspace module cosedaUI.map_window module cosedaUI.merging_window module cosedaUI.metadata_window module cosedaUI.peakfinder_window module cosedaUI.refinecenters_window module cosedaUI.strip_file_window module cosedaUI.unitcell_window module cosedaUI.update module cosedaUI.windowsettings module cosedaUI.workflow_wizzard module cosedaUI.workspace_functions module cosedaUI.workspace_unitcell_fit_window module create_index_dataset() (in module coseda.pipeline.strip_h5) create_insfile_mrc() (in module coseda.importers.import_mrc) create_insfiles() (in module coseda.initialize) (in module coseda.initialize.insfiles) create_insfiles_emd() (in module coseda.initialize) (in module coseda.initialize.insfiles) create_insfiles_gatan() (in module coseda.initialize) (in module coseda.initialize.insfiles) create_insfiles_mrc_batch() (in module coseda.importers.import_mrc) create_insfiles_tiff() (in module coseda.importers.import_tiff) create_layout() (cosedaUI.mainwindow.cosedaUI method) create_menu() (cosedaUI.mainwindow.cosedaUI method) create_overlay() (in module coseda.ici.overlay_elink) create_plain_insfile() (in module coseda.initialize) (in module coseda.initialize.insfiles) create_widgets() (cosedaUI.mainwindow.cosedaUI method) cross_correlate_lines() (in module coseda.map.findscanlines) crystfel_to_hklf4() (in module coseda.exporters.hklf4) crystfel_unique_axis_allowed() (in module coseda.crystfel_cell) cumulative_stats() (in module coseda.ici.summarize_image_run_log) D DaskClientManager (class in coseda.dask_client_manager) decimate() (in module cosedaUI.refinecenters_window) decode_column() (in module coseda.importers.import_velox) det_dx_mm (coseda.ici.evaluate_stream.ChunkRow attribute) det_dy_mm (coseda.ici.evaluate_stream.ChunkRow attribute) detect_latest_run_from_log() (in module coseda.ici.orchestrator) discover_workspace_unit_cell_streams() (in module coseda.unitcell_fit) Disk (class in coseda.map.mapping) display_log_file() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.workflow.WorkflowMixin method) (cosedaUI.mainwindow_sections.WorkflowMixin method) display_selected_plot() (cosedaUI.findcenters_window.CenterFinderSettingsWindow method) (cosedaUI.findcenters_window.PreviewWindow method) (cosedaUI.refinecenters_window.CenterRefinementSettingsWindow method) distance() (in module coseda.map.mapping) divide_into_batches() (in module coseda.centerfinding.findcenters_beamstop) dm4_folder_conversion() (in module coseda.importers.gatan_metareader) dm4_folder_conversion_batch() (in module coseda.importers.h5convert) dm4_to_h5() (in module coseda.importers.convert_dm4) do_init_sequence() (in module coseda.ici.orchestrator) done (coseda.ici.step1_hillmap_wrmsd.Step1Result attribute) done_stream_path() (in module coseda.ici.run_contract) dragEnterEvent() (cosedaUI.importers.import_emd_window.ImportEMDWindow method) (cosedaUI.importers.import_mrc_window.ImportMRCWindow method) (cosedaUI.importers.ImportEMDWindow method) (cosedaUI.importers.ImportMRCWindow method) (cosedaUI.mainwindow.IniListWidget method) dragMoveEvent() (cosedaUI.mainwindow.IniListWidget method) draw_peak_preview() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.viewer.ViewerMixin method) (cosedaUI.mainwindow_sections.ViewerMixin method) draw_pixmap_scalebar() (in module cosedaUI.image_tools) drop_amp_frac (coseda.ici.step1_hillmap_wrmsd.Step1Params attribute) dropEvent() (cosedaUI.importers.import_emd_window.ImportEMDWindow method) (cosedaUI.importers.import_mrc_window.ImportMRCWindow method) (cosedaUI.importers.ImportEMDWindow method) (cosedaUI.importers.ImportMRCWindow method) (cosedaUI.mainwindow.IniListWidget method) E early_break_stream_path() (in module coseda.ici.run_contract) emd_to_h5() (in module coseda.importers.h5convert) EMDImportThread (class in cosedaUI.importers.import_emd_window) emi_to_h5() (in module coseda.importers.h5convert) enable_opengl() (in module cosedaUI.mainwindow) ensure_atlas_for_current_file() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.viewer.ViewerMixin method) (cosedaUI.mainwindow_sections.ViewerMixin method) ensure_dense_logs() (in module coseda.nexus.logs) ensure_goniometer_transforms() (in module coseda.nexus.goniometer) ensure_image_key() (in module coseda.nexus.indices) ensure_image_nxdata() (in module coseda.nexus.images) ensure_index_dataset() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.workspace.WorkspaceMixin method) (cosedaUI.mainwindow_sections.WorkspaceMixin method) ensure_loaded() (cosedaUI.indexing_stream_manager.IndexingStreamManager method) ensure_nexus_parents() (in module coseda.nexus.groups) ensure_overlay_for_run() (in module coseda.ici.build_overlays_and_list) ensure_peak_nxdata() (in module coseda.nexus.peaks) envelope_downsample() (in module cosedaUI.refinecenters_window) error (cosedaUI.findcenters_window.Worker attribute) (cosedaUI.refinecenters_window.Worker attribute) event (coseda.ici.evaluate_stream.ChunkRow attribute) explore_floor (coseda.ici.step1_hillmap_wrmsd.Step1Params attribute) export_current_frame() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.viewer.ViewerMixin method) (cosedaUI.mainwindow_sections.ViewerMixin method) export_current_frame_as_shown() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.viewer.ViewerMixin method) (cosedaUI.mainwindow_sections.ViewerMixin method) export_display_image() (in module cosedaUI.image_tools) export_display_pixmap() (in module cosedaUI.image_tools) export_hdf5_images_to_tiff() (in module coseda.importers.import_velox) export_raw_image() (in module cosedaUI.image_tools) ExportMtzWindow (class in cosedaUI.export) extract_chunks_for_run() (in module coseda.ici.build_early_break_from_log) extract_frame_timestamp_from_gatan_metadata() (in module coseda.importers.gatan_metareader) extract_info_from_gatan_metadata() (in module coseda.importers.gatan_metareader) extract_info_from_mrc_metadata() (in module coseda.importers.import_mrc) extract_instrument_data() (in module coseda.importers.import_velox) extract_pos_data() (in module coseda.importers.import_velox) extract_stage_pos() (in module coseda.importers.import_velox) F failed (cosedaUI.aurora_window.AuroraPlotWorker attribute) (cosedaUI.h5_metadata_loader.H5MetadataLoader attribute) file_progress (cosedaUI.importers.import_emd_window.EMDImportThread attribute) (cosedaUI.importers.import_mrc_window.MRCImportThread attribute) (cosedaUI.strip_file_window.StripWorkerBatch attribute) file_progress_updated (cosedaUI.peakfinder_window.PeakFinderSettingsWindow attribute) files_dropped (cosedaUI.mainwindow.IniListWidget attribute) find_all_frames_ordered() (in module coseda.importers.gatan_metareader) find_chunk_with_reflections_from() (cosedaUI.indexing_stream_manager.IndexingStreamManager method) find_closest_available_frame() (cosedaUI.map_window.MapWindow method) find_closest_minimum() (in module coseda.map.findscanlines) find_closest_stroke() (in module coseda.map.findscanlines) find_clusters() (in module coseda.map.mapping) find_configfiles() (in module coseda.initialize) (in module coseda.initialize.project_files) find_dataset_paths() (in module coseda.importers.import_velox) find_friedel_pairs() (in module coseda.centerfinding.findcenters_beamstop) find_line_breaks() (in module coseda.map.findscanlines) find_matrix() (in module coseda.map.mapping) find_path_in_h5() (in module coseda.importers.import_velox) find_peaks_pf9() (in module coseda.peakfinding.peakfinder9) find_peaks_pf9_multiscale() (in module coseda.peakfinding.peakfinder9) find_primary_beam_direct() (in module coseda.centerfinding.findcenters_direct) find_seeds() (in module coseda.map.mapping) find_strokes_by_xpos() (in module coseda.map.findscanlines) find_strokes_by_ypos() (in module coseda.map.findscanlines) find_strongest_frame() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.viewer.ViewerMixin method) (cosedaUI.mainwindow_sections.ViewerMixin method) find_sweeps() (in module coseda.map.streaks) find_tiff_frame_files() (in module coseda.importers.import_tiff) find_touching_disks() (in module coseda.map.mapping) findpeaks8_batch() (in module coseda.peakfinding) (in module coseda.peakfinding.findpeaks) findpeaks9_dask_batch() (in module coseda.peakfinding.peakfinder9) findpeaks9_dask_file() (in module coseda.peakfinding.peakfinder9) findpeaks_dask_batch() (in module coseda.peakfinding) (in module coseda.peakfinding.findpeaks_dask) findpeaks_dask_file() (in module coseda.peakfinding) (in module coseda.peakfinding.findpeaks_dask) finished (cosedaUI.aurora_window.AuroraPlotWorker attribute) (cosedaUI.findcenters_window.Worker attribute) (cosedaUI.h5_metadata_loader.H5MetadataLoader attribute) (cosedaUI.ici_window.OrchestratorWorker attribute) (cosedaUI.importers.import_emd_window.EMDImportThread attribute) (cosedaUI.importers.import_mrc_window.MRCImportThread attribute) (cosedaUI.importers.import_tiff_window.TiffImportThread attribute) (cosedaUI.indexintegrate_sections.helpers.OrchestratorWorker attribute) (cosedaUI.indexintegrate_sections.OrchestratorWorker attribute) (cosedaUI.refinecenters_window.Worker attribute) (cosedaUI.strip_file_window.StripWorker attribute) (cosedaUI.strip_file_window.StripWorkerBatch attribute) first_attempt_center_mm (coseda.ici.step1_hillmap_wrmsd.Step1Params attribute) first_run_stats() (in module coseda.ici.summarize_image_run_log) fit_gaussian_to_largest_cluster() (in module coseda.centerfinding.findcenters_beamstop) fit_gaussian_to_values() (in module coseda.unitcell_fit) flush() (coseda.ici.orchestrator.TimestampingStream method) (cosedaUI.ici_window.GuiStream method) (cosedaUI.indexintegrate_sections.GuiStream method) (cosedaUI.indexintegrate_sections.helpers.GuiStream method) FocusableLineEdit (class in cosedaUI.findcenters_window) (class in cosedaUI.peakfinder_window) focusInEvent() (cosedaUI.findcenters_window.FocusableLineEdit method) (cosedaUI.peakfinder_window.FocusableLineEdit method) focusOutEvent() (cosedaUI.findcenters_window.FocusableLineEdit method) (cosedaUI.peakfinder_window.FocusableLineEdit method) G gaussian_curve() (in module coseda.unitcell_fit) generate_full_mask() (in module coseda.pixmask) generate_full_mask_hdf5() (in module coseda.pixmask) generate_mask() (in module coseda.pixmask) generate_parent_ini_file() (in module coseda.initialize) (in module coseda.initialize.project_files) GeomfileMixin (class in cosedaUI.indexintegrate_sections) (class in cosedaUI.indexintegrate_sections.geomfile) GeomfileWindow (class in cosedaUI.geomfile_window) get_available_intensity_datasets() (cosedaUI.map_window.MapWindow method) get_chunk_for_frame() (cosedaUI.indexing_stream_manager.IndexingStreamManager method) get_chunk_index() (cosedaUI.indexing_stream_manager.IndexingStreamManager method) get_chunks() (in module coseda.ici.evaluate_stream) get_client() (coseda.dask_client_manager.DaskClientManager class method) get_client_info() (coseda.dask_client_manager.DaskClientManager class method) get_dataset_chunk_info() (in module coseda.importers.import_h5) get_dir_size() (in module coseda.io) get_first_existing_path() (in module coseda.nexus.paths) get_frame_index_for_chunk() (cosedaUI.indexing_stream_manager.IndexingStreamManager method) get_frame_stack_shape() (in module coseda.centerfinding.findcenters_beamstop) get_free_space_unix() (in module coseda.io) get_free_space_windows() (in module coseda.io) get_goniometer_transform_order() (in module coseda.nexus.goniometer) get_image_mode() (in module coseda.importers.import_velox) get_last_chunk_with_reflections() (cosedaUI.indexing_stream_manager.IndexingStreamManager method) get_last_error() (cosedaUI.indexing_stream_manager.IndexingStreamManager method) get_line_bounds() (in module coseda.map.mapping) get_line_bounds_from_index() (in module coseda.map.findscanlines) get_logger() (in module coseda.logging_utils) get_mask_dataset() (in module coseda.nexus.paths) get_mrc_files() (in module coseda.importers.import_mrc) get_parameter_from_config() (cosedaUI.findcenters_window.CenterFinderSettingsWindow method) (cosedaUI.peakfinder_window.PeakFinderSettingsWindow method) (cosedaUI.refinecenters_window.CenterRefinementSettingsWindow method) get_parent_ini_file() (in module coseda.initialize) (in module coseda.initialize.project_files) get_parsed_stream() (cosedaUI.indexing_stream_manager.IndexingStreamManager method) get_pixels_per_meter() (in module coseda.centerfinding.findcenters_beamstop) get_reflections_for_frame() (cosedaUI.indexing_stream_manager.IndexingStreamManager method) get_stage_position() (in module coseda.importers.convert_dm4) get_stream_peaks_for_frame() (cosedaUI.indexing_stream_manager.IndexingStreamManager method) get_three_line_bounds() (in module coseda.map.findscanlines) get_timestamp_from_path() (in module coseda.importers.gatan_metareader) get_unique_alphatilts() (cosedaUI.map_window.MapWindow method) get_version_from_log() (in module cosedaUI.windowsettings) go_to_strongest_frame() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.viewer.ViewerMixin method) (cosedaUI.mainwindow_sections.ViewerMixin method) GuiStream (class in cosedaUI.ici_window) (class in cosedaUI.indexintegrate_sections) (class in cosedaUI.indexintegrate_sections.helpers) H H5MetadataLoader (class in cosedaUI.h5_metadata_loader) handle_image_update() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.viewer.ViewerMixin method) (cosedaUI.mainwindow_sections.ViewerMixin method) handle_input() (in module coseda.initialize) (in module coseda.io) handle_print_option_change() (cosedaUI.map_window.MapWindow method) has_chunks() (cosedaUI.indexing_stream_manager.IndexingStreamManager method) has_common_angle() (in module coseda.map.mapping) has_detector_shift() (in module cosedaUI.workflow_wizzard) has_mask_dataset() (in module cosedaUI.workflow_wizzard) has_parser() (cosedaUI.indexing_stream_manager.IndexingStreamManager method) has_peak_dataset() (in module cosedaUI.workflow_wizzard) has_stream_file() (cosedaUI.indexing_stream_manager.IndexingStreamManager method) hasHeightForWidth() (cosedaUI.mainwindow.AspectRatioWidget method) hdf5_path (cosedaUI.aurora_window.AuroraPlotWindow property) heightForWidth() (cosedaUI.mainwindow.AspectRatioWidget method) highlight_selected_file() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.workspace.WorkspaceMixin method) (cosedaUI.mainwindow_sections.WorkspaceMixin method) hill_amp_frac (coseda.ici.step1_hillmap_wrmsd.Step1Params attribute) hkl2mtz() (in module coseda.export) hovered (cosedaUI.image_tools.HoverLabel attribute) HoverLabel (class in cosedaUI.image_tools) I IciMixin (class in cosedaUI.indexintegrate_sections) (class in cosedaUI.indexintegrate_sections.ici) image (coseda.ici.evaluate_stream.ChunkRow attribute) image_bit_depth_label() (in module coseda.peakfinding.aurora) ImageInspector (class in cosedaUI.image_tools) import_finished() (cosedaUI.importers.import_emd_window.ImportEMDWindow method) (cosedaUI.importers.import_mrc_window.ImportMRCWindow method) (cosedaUI.importers.import_tiff_window.ImportTiffWindow method) (cosedaUI.importers.ImportEMDWindow method) (cosedaUI.importers.ImportMRCWindow method) (cosedaUI.importers.ImportTiffWindow method) import_h5() (cosedaUI.importers.import_h5_window.ImportH5Window method) (cosedaUI.importers.ImportH5Window method) ImportEMDWindow (class in cosedaUI.importers) (class in cosedaUI.importers.import_emd_window) ImportH5Window (class in cosedaUI.importers) (class in cosedaUI.importers.import_h5_window) ImportMixin (class in cosedaUI.mainwindow_sections) (class in cosedaUI.mainwindow_sections.imports) ImportMRCWindow (class in cosedaUI.importers) (class in cosedaUI.importers.import_mrc_window) ImportTiffWindow (class in cosedaUI.importers) (class in cosedaUI.importers.import_tiff_window) indexed (coseda.ici.evaluate_stream.ChunkRow attribute) (coseda.ici.step1_hillmap_wrmsd.Trial attribute) (coseda.ici.summarize_image_run_log.Trial attribute) IndexingControlWindow (class in cosedaUI.indexintegrate_window) IndexingControlWindow.ProcessOutputThread (class in cosedaUI.indexintegrate_window) IndexingMixin (class in cosedaUI.mainwindow_sections) (class in cosedaUI.mainwindow_sections.indexing) IndexingStreamManager (class in cosedaUI.indexing_stream_manager) IndexSettingsMixin (class in cosedaUI.indexintegrate_sections) (class in cosedaUI.indexintegrate_sections.index_settings) ini_path (coseda.unitcell_fit.WorkspaceStreamSource attribute) ini_selection_changed (cosedaUI.indexintegrate_window.IndexingControlWindow attribute) (cosedaUI.mainwindow.cosedaUI attribute) IniListWidget (class in cosedaUI.mainwindow) init_ui() (cosedaUI.about_window.AboutWindow method) (cosedaUI.findcenters_window.CenterFinderSettingsWindow method) (cosedaUI.importers.import_emd_window.ImportEMDWindow method) (cosedaUI.importers.import_mrc_window.ImportMRCWindow method) (cosedaUI.importers.import_tiff_window.ImportTiffWindow method) (cosedaUI.importers.ImportEMDWindow method) (cosedaUI.importers.ImportMRCWindow method) (cosedaUI.importers.ImportTiffWindow method) (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.map_window.MapWindow method) (cosedaUI.peakfinder_window.PeakFinderSettingsWindow method) (cosedaUI.refinecenters_window.CenterRefinementSettingsWindow method) interlacecorrection() (in module coseda.map.mapping) interpolate_centers() (in module coseda.centerfinding.findcenters_direct) is_dataset_chunked_first_dim() (in module coseda.importers.import_h5) is_loaded() (cosedaUI.indexing_stream_manager.IndexingStreamManager method) is_metadata_complete() (cosedaUI.metadata_window.MetadataWindow method) is_parent_config_file() (in module coseda.initialize) (in module coseda.io) is_stream_available() (cosedaUI.indexing_stream_manager.IndexingStreamManager method) is_within_bounds() (in module coseda.centerfinding.findcenters_direct) iter_records() (in module coseda.ici.extract_mille_shifts) iterate_until_done() (in module coseda.ici.orchestrator) iterative_gaussian_fitting_on_subset() (in module coseda.centerfinding.findcenters_beamstop) K keyPressEvent() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.viewer.ViewerMixin method) (cosedaUI.mainwindow_sections.ViewerMixin method) kill_all_dask_clusters() (coseda.dask_client_manager.DaskClientManager class method) kill_current_cluster() (coseda.dask_client_manager.DaskClientManager class method) L latest_run() (in module coseda.ici.orchestrator) linearize_map() (in module coseda.map.mapping) list_run_numbers() (in module coseda.ici.orchestrator) load_and_print_acquisition_details() (cosedaUI.metadata_window.MetadataWindow method) load_and_process_batch() (in module coseda.peakfinding.findpeaks_dask) load_atlas() (in module coseda.map.streaks) load_changelog() (in module cosedaUI.windowsettings) load_detector_geometry() (in module coseda.detector_geometry) load_image_from_hdf5() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.viewer.ViewerMixin method) (cosedaUI.mainwindow_sections.ViewerMixin method) load_last_directory() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.workspace.WorkspaceMixin method) (cosedaUI.mainwindow_sections.WorkspaceMixin method) (in module cosedaUI.workspace_functions) load_last_workspace_state() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.workspace.WorkspaceMixin method) (cosedaUI.mainwindow_sections.WorkspaceMixin method) (in module cosedaUI.workspace_functions) load_mask_hdf5() (in module coseda.pixmask) load_or_compute_aurora_points() (in module coseda.peakfinding.aurora) load_sidecar() (in module coseda.ici.summarize_image_run_log) load_state() (in module coseda.ici.build_early_break_from_log) (in module coseda.ici.build_overlays_and_list) (in module coseda.ici.propose_next_shifts) log_client_info() (coseda.dask_client_manager.DaskClientManager class method) log_print() (in module coseda.logging_utils) log_result() (in module coseda.initialize) (in module coseda.logging_utils) log_start() (in module coseda.initialize) (in module coseda.logging_utils) lowess_xunit() (in module coseda.centerrefinement.refinecenters_direct) M main() (in module coseda.exporters.hklf4) (in module coseda.ici.build_early_break_from_log) (in module coseda.ici.build_overlays_and_list) (in module coseda.ici.create_run_sh) (in module coseda.ici.evaluate_stream) (in module coseda.ici.extract_mille_shifts) (in module coseda.ici.fix_stream_paths) (in module coseda.ici.no_run_prep_singlelist) (in module coseda.ici.orchestrator) (in module coseda.ici.propose_next_shifts) (in module coseda.ici.run_sh) (in module coseda.ici.summarize_image_run_log) (in module coseda.ici.update_image_run_log_grouped) (in module cosedaUI.ici_window) manifest_path() (in module coseda.ici.run_contract) map_chunk_ids_by_image_event() (in module coseda.ici.build_early_break_from_log) MapWindow (class in cosedaUI.map_window) MAX_INDEXER_THREADS (cosedaUI.indexintegrate_sections.index_settings.IndexSettingsMixin attribute) (cosedaUI.indexintegrate_sections.IndexSettingsMixin attribute) (cosedaUI.indexintegrate_window.IndexingControlWindow attribute) MergingSettingsWindow (class in cosedaUI.merging_window) MetadataWindow (class in cosedaUI.metadata_window) min_spacing_mm (coseda.ici.step1_hillmap_wrmsd.Step1Params attribute) minimumSizeHint() (cosedaUI.mainwindow.AspectRatioWidget method) module coseda coseda.centerfinding coseda.centerfinding.findcenters_beamstop coseda.centerfinding.findcenters_direct coseda.centerrefinement coseda.centerrefinement.cancellation coseda.centerrefinement.refinecenters_beamstop coseda.centerrefinement.refinecenters_direct coseda.crystfel_cell coseda.dask_client_manager coseda.detector_geometry coseda.export coseda.exporters.hklf4 coseda.geomfile coseda.ici coseda.ici.build_early_break_from_log coseda.ici.build_overlays_and_list coseda.ici.create_run_sh coseda.ici.evaluate_stream coseda.ici.extract_mille_shifts coseda.ici.fix_stream_paths coseda.ici.no_run_prep_singlelist coseda.ici.orchestrator coseda.ici.overlay_elink coseda.ici.propose_next_shifts coseda.ici.run_contract coseda.ici.run_sh coseda.ici.step1_hillmap_wrmsd coseda.ici.step2_dxdy coseda.ici.summarize_image_run_log coseda.ici.update_image_run_log_grouped coseda.importers coseda.importers.convert_dm4 coseda.importers.gatan_metareader coseda.importers.h5convert coseda.importers.import_h5 coseda.importers.import_mrc coseda.importers.import_tiff coseda.importers.import_velox coseda.indexintegrate coseda.initialize coseda.initialize.insfiles coseda.initialize.project_files coseda.initialize.settings coseda.io coseda.logging_utils coseda.map coseda.map.findscanlines coseda.map.mapping coseda.map.streaks coseda.merge coseda.nexus coseda.nexus.detector coseda.nexus.goniometer coseda.nexus.groups coseda.nexus.images coseda.nexus.indices coseda.nexus.logs coseda.nexus.paths coseda.nexus.peaks coseda.nexus.process coseda.peakfinding coseda.peakfinding.aurora coseda.peakfinding.findpeaks coseda.peakfinding.findpeaks_dask coseda.peakfinding.maxres coseda.peakfinding.peakfinder9 coseda.pipeline coseda.pipeline.frame_intensities coseda.pipeline.processimage coseda.pipeline.strip_h5 coseda.pixmask coseda.unitcell_fit cosedaUI cosedaUI.about_window cosedaUI.aurora_window cosedaUI.cellfile_window cosedaUI.export cosedaUI.findcenters_window cosedaUI.geomfile_window cosedaUI.h5_metadata_loader cosedaUI.ici_window cosedaUI.image_tools cosedaUI.importers cosedaUI.importers.import_emd_window cosedaUI.importers.import_h5_window cosedaUI.importers.import_mrc_window cosedaUI.importers.import_tiff_window cosedaUI.indexing_stream_manager cosedaUI.indexintegrate_sections cosedaUI.indexintegrate_sections.cellfile cosedaUI.indexintegrate_sections.geomfile cosedaUI.indexintegrate_sections.helpers cosedaUI.indexintegrate_sections.ici cosedaUI.indexintegrate_sections.index_settings cosedaUI.indexintegrate_sections.run_control cosedaUI.indexintegrate_window cosedaUI.mainwindow cosedaUI.mainwindow_sections cosedaUI.mainwindow_sections.cluster cosedaUI.mainwindow_sections.imports cosedaUI.mainwindow_sections.indexing cosedaUI.mainwindow_sections.viewer cosedaUI.mainwindow_sections.workflow cosedaUI.mainwindow_sections.workspace cosedaUI.map_window cosedaUI.merging_window cosedaUI.metadata_window cosedaUI.peakfinder_window cosedaUI.refinecenters_window cosedaUI.strip_file_window cosedaUI.unitcell_window cosedaUI.update cosedaUI.windowsettings cosedaUI.workflow_wizzard cosedaUI.workspace_functions cosedaUI.workspace_unitcell_fit_window mouseMoveEvent() (cosedaUI.image_tools.HoverLabel method) mouseReleaseEvent() (cosedaUI.refinecenters_window.ClickableLabel method) move_plain_h5() (in module coseda.importers.import_h5) moving_average() (in module coseda.map.findscanlines) mrc_folder_conversion() (in module coseda.importers.import_mrc) mrc_folder_conversion_batch() (in module coseda.importers.import_mrc) MRCImportThread (class in cosedaUI.importers.import_mrc_window) N n_candidates (coseda.ici.step1_hillmap_wrmsd.Step1Params attribute) n_kept (coseda.ici.evaluate_stream.ChunkRow attribute) n_matches (coseda.ici.evaluate_stream.ChunkRow attribute) new_workspace() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.workspace.WorkspaceMixin method) (cosedaUI.mainwindow_sections.WorkspaceMixin method) (in module cosedaUI.workspace_functions) next_dx (coseda.ici.summarize_image_run_log.Trial attribute) next_dy (coseda.ici.summarize_image_run_log.Trial attribute) next_frame() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.viewer.ViewerMixin method) (cosedaUI.mainwindow_sections.ViewerMixin method) normalize_crystfel_lattice_type() (in module coseda.crystfel_cell) normalize_dataset_path() (in module coseda.nexus.paths) NumericSortTreeWidgetItem (class in cosedaUI.findcenters_window) O on_backlash_offset_changed() (cosedaUI.map_window.MapWindow method) on_crystallinity_checkbox_toggle() (cosedaUI.map_window.MapWindow method) on_crystallinity_threshold_changed() (cosedaUI.map_window.MapWindow method) on_detector_changed() (cosedaUI.metadata_window.PixelCalcDialog method) on_empty_only_checkbox_changed() (cosedaUI.strip_file_window.StripFilesWindow method) on_field_focused() (cosedaUI.findcenters_window.CenterFinderSettingsWindow method) (cosedaUI.peakfinder_window.PeakFinderSettingsWindow method) on_file_progress_updated() (cosedaUI.peakfinder_window.PeakFinderSettingsWindow method) on_find_centers_all() (cosedaUI.findcenters_window.CenterFinderSettingsWindow method) on_find_centers_current() (cosedaUI.findcenters_window.CenterFinderSettingsWindow method) on_find_peaks_all() (cosedaUI.peakfinder_window.PeakFinderSettingsWindow method) on_find_peaks_current() (cosedaUI.peakfinder_window.PeakFinderSettingsWindow method) on_find_refinement_all() (cosedaUI.refinecenters_window.CenterRefinementSettingsWindow method) on_find_refinement_current() (cosedaUI.refinecenters_window.CenterRefinementSettingsWindow method) on_force_linear_toggled() (cosedaUI.findcenters_window.CenterFinderSettingsWindow method) on_frame_order_changed() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.viewer.ViewerMixin method) (cosedaUI.mainwindow_sections.ViewerMixin method) on_generate_full_mask_clicked() (cosedaUI.metadata_window.MetadataWindow method) on_hover() (cosedaUI.map_window.MapWindow method) on_image_click() (cosedaUI.map_window.MapWindow method) on_indexing_run_stream_changed() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.indexing.IndexingMixin method) (cosedaUI.mainwindow_sections.IndexingMixin method) on_indexintegrate_requested_select_ini() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.workspace.WorkspaceMixin method) (cosedaUI.mainwindow_sections.WorkspaceMixin method) on_ini_select() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.workspace.WorkspaceMixin method) (cosedaUI.mainwindow_sections.WorkspaceMixin method) on_kill_all_clusters() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.cluster.ClusterMixin method) (cosedaUI.mainwindow_sections.ClusterMixin method) on_kill_current_cluster() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.cluster.ClusterMixin method) (cosedaUI.mainwindow_sections.ClusterMixin method) on_method_change() (cosedaUI.findcenters_window.CenterFinderSettingsWindow method) (cosedaUI.refinecenters_window.CenterRefinementSettingsWindow method) on_mouse_move() (cosedaUI.image_tools.ImageInspector method) on_mouse_press() (cosedaUI.image_tools.ImageInspector method) on_mouse_release() (cosedaUI.image_tools.ImageInspector method) on_next() (cosedaUI.refinecenters_window.PreviewWindow method) on_open_dashboard() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.cluster.ClusterMixin method) (cosedaUI.mainwindow_sections.ClusterMixin method) on_peakfinding_error() (cosedaUI.peakfinder_window.PeakFinderSettingsWindow method) on_peakfinding_finished() (cosedaUI.peakfinder_window.PeakFinderSettingsWindow method) on_pixelmask_btn_clicked() (cosedaUI.metadata_window.MetadataWindow method) on_plot_display_label_clicked() (cosedaUI.refinecenters_window.CenterRefinementSettingsWindow method) on_plot_histogram() (cosedaUI.peakfinder_window.PeakFinderSettingsWindow method) on_prev() (cosedaUI.refinecenters_window.PreviewWindow method) on_processing_cancelled() (cosedaUI.findcenters_window.CenterFinderSettingsWindow method) on_processing_error() (cosedaUI.findcenters_window.CenterFinderSettingsWindow method) on_processing_finished() (cosedaUI.findcenters_window.CenterFinderSettingsWindow method) on_progress_done() (cosedaUI.ici_window.OrchestratorWidget method) on_progress_init() (cosedaUI.ici_window.OrchestratorWidget method) on_progress_step() (cosedaUI.ici_window.OrchestratorWidget method) on_progress_updated() (cosedaUI.findcenters_window.CenterFinderSettingsWindow method) (cosedaUI.peakfinder_window.PeakFinderSettingsWindow method) on_refinement_cancelled() (cosedaUI.refinecenters_window.CenterRefinementSettingsWindow method) on_refinement_error() (cosedaUI.refinecenters_window.CenterRefinementSettingsWindow method) on_refinement_finished() (cosedaUI.refinecenters_window.CenterRefinementSettingsWindow method) on_remove_mask_clicked() (cosedaUI.metadata_window.MetadataWindow method) on_run_clicked() (cosedaUI.ici_window.OrchestratorWidget method) on_run_selected() (cosedaUI.refinecenters_window.PreviewWindow method) on_save_all() (cosedaUI.findcenters_window.CenterFinderSettingsWindow method) (cosedaUI.peakfinder_window.PeakFinderSettingsWindow method) (cosedaUI.refinecenters_window.CenterRefinementSettingsWindow method) on_save_current() (cosedaUI.findcenters_window.CenterFinderSettingsWindow method) (cosedaUI.peakfinder_window.PeakFinderSettingsWindow method) (cosedaUI.refinecenters_window.CenterRefinementSettingsWindow method) on_set_cluster_address() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.cluster.ClusterMixin method) (cosedaUI.mainwindow_sections.ClusterMixin method) on_setting_changed() (cosedaUI.peakfinder_window.PeakFinderSettingsWindow method) on_show_strong_peaks_toggled() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.viewer.ViewerMixin method) (cosedaUI.mainwindow_sections.ViewerMixin method) on_skip_linear_toggled() (cosedaUI.findcenters_window.CenterFinderSettingsWindow method) on_slider_release() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.viewer.ViewerMixin method) (cosedaUI.mainwindow_sections.ViewerMixin method) on_slider_start() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.viewer.ViewerMixin method) (cosedaUI.mainwindow_sections.ViewerMixin method) on_stop_clicked() (cosedaUI.findcenters_window.CenterFinderSettingsWindow method) (cosedaUI.ici_window.OrchestratorWidget method) (cosedaUI.refinecenters_window.CenterRefinementSettingsWindow method) on_toggle_indexing_results() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.indexing.IndexingMixin method) (cosedaUI.mainwindow_sections.IndexingMixin method) on_vdf_overlay_toggled() (cosedaUI.map_window.MapWindow method) on_vdf_slider_changed() (cosedaUI.map_window.MapWindow method) on_worker_finished() (cosedaUI.ici_window.OrchestratorWidget method) open_about_window() (in module cosedaUI.about_window) open_aurora_plot() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.viewer.ViewerMixin method) (cosedaUI.mainwindow_sections.ViewerMixin method) open_centerfinder_settings_window() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.workspace.WorkspaceMixin method) (cosedaUI.mainwindow_sections.WorkspaceMixin method) open_centerrefinement_settings_window() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.workspace.WorkspaceMixin method) (cosedaUI.mainwindow_sections.WorkspaceMixin method) open_check_metadata_window() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.workflow.WorkflowMixin method) (cosedaUI.mainwindow_sections.WorkflowMixin method) open_export_window() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.workflow.WorkflowMixin method) (cosedaUI.mainwindow_sections.WorkflowMixin method) open_file() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.workspace.WorkspaceMixin method) (cosedaUI.mainwindow_sections.WorkspaceMixin method) open_import_emd_window() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.ImportMixin method) (cosedaUI.mainwindow_sections.imports.ImportMixin method) open_import_h5_window() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.ImportMixin method) (cosedaUI.mainwindow_sections.imports.ImportMixin method) open_import_mrc_window() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.ImportMixin method) (cosedaUI.mainwindow_sections.imports.ImportMixin method) open_import_tiff_window() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.ImportMixin method) (cosedaUI.mainwindow_sections.imports.ImportMixin method) open_index_integrate_window() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.workflow.WorkflowMixin method) (cosedaUI.mainwindow_sections.WorkflowMixin method) open_index_window() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.workflow.WorkflowMixin method) (cosedaUI.mainwindow_sections.WorkflowMixin method) open_map() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.viewer.ViewerMixin method) (cosedaUI.mainwindow_sections.ViewerMixin method) open_merge_window() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.workflow.WorkflowMixin method) (cosedaUI.mainwindow_sections.WorkflowMixin method) open_peakfinder_settings_window() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.workspace.WorkspaceMixin method) (cosedaUI.mainwindow_sections.WorkspaceMixin method) open_pixel_calc_dialog() (cosedaUI.metadata_window.MetadataWindow method) open_plot_image() (cosedaUI.refinecenters_window.CenterRefinementSettingsWindow method) open_popup() (cosedaUI.image_tools.ImageInspector method) open_strip_files_window() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.workflow.WorkflowMixin method) (cosedaUI.mainwindow_sections.WorkflowMixin method) open_unit_cell_hist_window() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.workflow.WorkflowMixin method) (cosedaUI.mainwindow_sections.WorkflowMixin method) open_workspace() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.workspace.WorkspaceMixin method) (cosedaUI.mainwindow_sections.WorkspaceMixin method) (in module cosedaUI.workspace_functions) open_workspace_unit_cell_fit_window() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.workflow.WorkflowMixin method) (cosedaUI.mainwindow_sections.WorkflowMixin method) OrchestratorMainWindow (class in cosedaUI.ici_window) OrchestratorRunLogger (class in coseda.ici.orchestrator) OrchestratorWidget (class in cosedaUI.ici_window) OrchestratorWorker (class in cosedaUI.ici_window) (class in cosedaUI.indexintegrate_sections) (class in cosedaUI.indexintegrate_sections.helpers) output() (in module coseda.centerrefinement.refinecenters_beamstop) output_direct() (in module coseda.centerrefinement.refinecenters_direct) output_received (cosedaUI.indexintegrate_window.IndexingControlWindow.ProcessOutputThread attribute) P parse_blocks() (in module coseda.ici.propose_next_shifts) parse_chunk_text() (in module coseda.ici.evaluate_stream) parse_config() (in module coseda.initialize) (in module coseda.io) parse_dm4_metadata() (in module coseda.importers.gatan_metareader) parse_log() (in module coseda.ici.build_overlays_and_list) parse_log_rows() (in module coseda.ici.summarize_image_run_log) parse_scaling_file() (in module coseda.merge) parse_stream_chunks() (in module coseda.ici.build_early_break_from_log) parse_workspace_cell() (in module coseda.unitcell_fit) PeakFinderSettingsWindow (class in cosedaUI.peakfinder_window) peakfinding_error (cosedaUI.peakfinder_window.PeakFinderSettingsWindow attribute) peakfinding_stats() (in module coseda.peakfinding.findpeaks_dask) per_frame_two_globals() (in module coseda.ici.extract_mille_shifts) perform_lowess() (in module coseda.centerrefinement.refinecenters_beamstop) PixelCalcDialog (class in cosedaUI.metadata_window) plot_4Dstem() (in module coseda.importers.import_velox) plot_batch_centers() (in module coseda.centerfinding.findcenters_beamstop) plot_clusters() (in module coseda.map.mapping) plot_comparison() (in module coseda.pixmask) plot_correlation() (in module coseda.map.findscanlines) plot_crystamorphus() (in module coseda.importers.import_velox) plot_crystamorphusvac() (in module coseda.map.mapping) plot_crystamorphusvac_overlap() (in module coseda.map.mapping) plot_data() (cosedaUI.map_window.MapWindow method) plot_deviation_cloud() (in module coseda.centerfinding.findcenters_beamstop) plot_deviations() (in module coseda.centerrefinement.refinecenters_beamstop) plot_line_profiles() (in module coseda.map.findscanlines) plot_linear_fit() (in module coseda.centerfinding.findcenters_beamstop) plot_lowess_and_centers() (in module coseda.centerrefinement.refinecenters_beamstop) plot_map_peaks() (in module coseda.map.mapping) plot_nPeaks_histogram() (in module coseda.map.mapping) plot_rasterized_map() (in module coseda.map.streaks) plot_stagepos_y_with_breaks() (in module coseda.map.findscanlines) plot_stagepos_y_with_breaks_debug() (in module coseda.map.findscanlines) point_clicked_signal (cosedaUI.map_window.MapWindow attribute) PreviewWindow (class in cosedaUI.findcenters_window) (class in cosedaUI.refinecenters_window) previous_frame() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.viewer.ViewerMixin method) (cosedaUI.mainwindow_sections.ViewerMixin method) process_and_save_h5() (in module coseda.importers.convert_dm4) process_batch() (in module coseda.centerfinding.findcenters_beamstop) (in module coseda.peakfinding.findpeaks) process_centers() (in module coseda.centerfinding.findcenters_direct) process_file() (in module coseda.peakfinding.findpeaks) process_image() (in module coseda.peakfinding.findpeaks) (in module coseda.pipeline) (in module coseda.pipeline.processimage) process_single_frame() (in module coseda.peakfinding) (in module coseda.peakfinding.findpeaks) progress (cosedaUI.aurora_window.AuroraPlotWorker attribute) (cosedaUI.findcenters_window.Worker attribute) (cosedaUI.strip_file_window.StripWorker attribute) (cosedaUI.strip_file_window.StripWorkerBatch attribute) progress_init (cosedaUI.ici_window.OrchestratorWorker attribute) (cosedaUI.indexintegrate_sections.helpers.OrchestratorWorker attribute) (cosedaUI.indexintegrate_sections.OrchestratorWorker attribute) progress_step (cosedaUI.ici_window.OrchestratorWorker attribute) (cosedaUI.indexintegrate_sections.helpers.OrchestratorWorker attribute) (cosedaUI.indexintegrate_sections.OrchestratorWorker attribute) progress_updated (cosedaUI.findcenters_window.CenterFinderSettingsWindow attribute) (cosedaUI.peakfinder_window.PeakFinderSettingsWindow attribute) proposal_counts_for_run() (in module coseda.ici.summarize_image_run_log) proposal_xy_mm (coseda.ici.step1_hillmap_wrmsd.Step1Result attribute) propose_event() (in module coseda.ici.propose_next_shifts) propose_step1() (in module coseda.ici.step1_hillmap_wrmsd) propose_step2_dxdy() (in module coseda.ici.step2_dxdy) Q quadrant_var_cost() (in module coseda.centerrefinement.refinecenters_direct) quadrant_variance_numba() (in module coseda.centerrefinement.refinecenters_direct) quartering() (in module coseda.centerfinding.findcenters_beamstop) quartering_batch() (in module coseda.centerfinding.findcenters_beamstop) R radius_mm (coseda.ici.step1_hillmap_wrmsd.Step1Params attribute) rasterize_arrays() (in module coseda.map.streaks) rasterize_map() (in module coseda.map.streaks) raw_to_corrected() (in module coseda.detector_geometry) raw_to_corrected_points() (in module coseda.detector_geometry) read_config() (in module coseda.initialize) (in module coseda.io) read_log() (in module coseda.ici.propose_next_shifts) reason (coseda.ici.evaluate_stream.ChunkRow attribute) (coseda.ici.step1_hillmap_wrmsd.Step1Result attribute) receive_coordinate() (cosedaUI.findcenters_window.CenterFinderSettingsWindow method) (cosedaUI.peakfinder_window.PeakFinderSettingsWindow method) refine() (in module coseda.centerrefinement.refinecenters_beamstop) refine_and_update_centers() (in module coseda.centerrefinement.refinecenters_direct) refine_center_with_friedel() (in module coseda.centerfinding.findcenters_beamstop) refine_center_with_friedel_and_update() (in module coseda.centerrefinement.refinecenters_beamstop) refine_center_with_friedel_batch() (in module coseda.centerrefinement.refinecenters_beamstop) refine_clusters() (in module coseda.map.mapping) refine_direct_all() (in module coseda.centerrefinement.refinecenters_direct) refine_direct_batch() (in module coseda.centerrefinement.refinecenters_direct) refine_direct_single_frame() (in module coseda.centerrefinement.refinecenters_direct) refine_stagepos_x() (in module coseda.importers.import_velox) refinecenters_batch() (in module coseda.centerrefinement.refinecenters_beamstop) refinecenters_direct_batch() (in module coseda.centerrefinement.refinecenters_direct) refinecenters_direct_file() (in module coseda.centerrefinement.refinecenters_direct) RefinementCancelled reload_current_file() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.workspace.WorkspaceMixin method) (cosedaUI.mainwindow_sections.WorkspaceMixin method) reload_file_preserve_frame() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.workspace.WorkspaceMixin method) (cosedaUI.mainwindow_sections.WorkspaceMixin method) remap_framestack() (in module coseda.importers.import_velox) remove_ini_files() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.workspace.WorkspaceMixin method) (cosedaUI.mainwindow_sections.WorkspaceMixin method) (in module cosedaUI.workspace_functions) remove_mask_hdf5() (in module coseda.pixmask) remove_selected_folders() (cosedaUI.importers.import_mrc_window.ImportMRCWindow method) (cosedaUI.importers.ImportMRCWindow method) remove_selected_items() (cosedaUI.importers.import_emd_window.ImportEMDWindow method) (cosedaUI.importers.ImportEMDWindow method) repack_hdf5_with_backup() (in module coseda.pipeline.strip_h5) report_issue() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.workflow.WorkflowMixin method) (cosedaUI.mainwindow_sections.WorkflowMixin method) request_cancel() (cosedaUI.findcenters_window.Worker method) (cosedaUI.refinecenters_window.Worker method) request_stop_on_close() (cosedaUI.ici_window.OrchestratorWidget method) reset_for_new_hdf5() (cosedaUI.indexing_stream_manager.IndexingStreamManager method) resizeEvent() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.viewer.ViewerMixin method) (cosedaUI.mainwindow_sections.ViewerMixin method) (cosedaUI.map_window.MapWindow method) resolve_final_stream_path() (in module coseda.ici.run_contract) resolve_frame_dataset() (in module coseda.centerfinding.findcenters_beamstop) resolve_loess_span() (in module coseda.centerrefinement.refinecenters_direct) resolve_real_source() (in module coseda.ici.update_image_run_log_grouped) resolve_stream_path_for_run() (in module coseda.unitcell_fit) resume_processing() (in module coseda.initialize) (in module coseda.initialize.project_files) rng_seed (coseda.ici.step1_hillmap_wrmsd.Step1Params attribute) run (coseda.ici.summarize_image_run_log.Trial attribute) run() (cosedaUI.aurora_window.AuroraPlotWorker method) (cosedaUI.findcenters_window.Worker method) (cosedaUI.h5_metadata_loader.H5MetadataLoader method) (cosedaUI.ici_window.OrchestratorWorker method) (cosedaUI.importers.import_emd_window.EMDImportThread method) (cosedaUI.importers.import_mrc_window.MRCImportThread method) (cosedaUI.importers.import_tiff_window.TiffImportThread method) (cosedaUI.indexintegrate_sections.helpers.OrchestratorWorker method) (cosedaUI.indexintegrate_sections.OrchestratorWorker method) (cosedaUI.indexintegrate_window.IndexingControlWindow.ProcessOutputThread method) (cosedaUI.refinecenters_window.Worker method) (cosedaUI.strip_file_window.StripWorker method) (cosedaUI.strip_file_window.StripWorkerBatch method) run_app() (in module cosedaUI.mainwindow) run_base_candidates_for_ini() (in module coseda.unitcell_fit) run_dir (coseda.unitcell_fit.WorkspaceStreamSource attribute) run_findcenters_direct() (in module coseda.centerfinding.findcenters_direct) run_findpeaks() (cosedaUI.peakfinder_window.PeakFinderSettingsWindow method) run_index_and_integrate() (in module coseda.indexintegrate) run_merging() (in module coseda.merge) run_name() (in module coseda.ici.run_contract) run_one_event() (in module coseda.ici.run_sh) run_py() (in module coseda.ici.orchestrator) run_root_path() (in module coseda.ici.run_contract) run_stream_path() (in module coseda.ici.build_early_break_from_log) RunControlMixin (class in cosedaUI.indexintegrate_sections) (class in cosedaUI.indexintegrate_sections.run_control) runs_dir() (in module coseda.ici.orchestrator) S save_4Dstem() (in module coseda.importers.import_velox) save_acceleration_voltage() (cosedaUI.metadata_window.MetadataWindow method) save_atlas() (in module coseda.map.streaks) save_camera_length_correction() (cosedaUI.metadata_window.MetadataWindow method) save_cell_file() (cosedaUI.cellfile_window.CellfileWindow method) save_mask_hdf5() (in module coseda.pixmask) save_metadata_field() (cosedaUI.metadata_window.MetadataWindow method) save_pixels_per_meter() (cosedaUI.metadata_window.MetadataWindow method) save_state() (in module coseda.ici.propose_next_shifts) save_workspace() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.workspace.WorkspaceMixin method) (cosedaUI.mainwindow_sections.WorkspaceMixin method) (in module cosedaUI.workspace_functions) save_workspace_state() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.workspace.WorkspaceMixin method) (cosedaUI.mainwindow_sections.WorkspaceMixin method) (in module cosedaUI.workspace_functions) select_tiff_folder() (cosedaUI.importers.import_tiff_window.ImportTiffWindow method) (cosedaUI.importers.ImportTiffWindow method) set_aspect_ratio() (cosedaUI.mainwindow.AspectRatioWidget method) set_center_based_on_batch() (in module coseda.centerfinding.findcenters_beamstop) set_center_based_on_line_fit() (in module coseda.centerfinding.findcenters_beamstop) set_hdf5_path() (cosedaUI.map_window.MapWindow method) set_run() (cosedaUI.findcenters_window.PreviewWindow method) set_scheduler_address() (coseda.dask_client_manager.DaskClientManager class method) set_stream_path() (cosedaUI.indexing_stream_manager.IndexingStreamManager method) (cosedaUI.unitcell_window.UnitCellHistogramWindow method) set_style() (in module cosedaUI.windowsettings) set_tiffconversion_parameters() (in module coseda.importers.import_tiff) set_vdf_overlay() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.viewer.ViewerMixin method) (cosedaUI.mainwindow_sections.ViewerMixin method) set_workspace_context() (cosedaUI.workspace_unitcell_fit_window.WorkspaceUnitCellFitWindow method) set_workspace_ini_paths() (cosedaUI.workspace_unitcell_fit_window.WorkspaceUnitCellFitWindow method) settings_applied (cosedaUI.findcenters_window.CenterFinderSettingsWindow attribute) (cosedaUI.peakfinder_window.PeakFinderSettingsWindow attribute) shoutout() (in module coseda.initialize) (in module coseda.logging_utils) show_about_window() (cosedaUI.mainwindow.cosedaUI method) show_latest_indexed_frame() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.indexing.IndexingMixin method) (cosedaUI.mainwindow_sections.IndexingMixin method) show_next_indexed_frame() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.indexing.IndexingMixin method) (cosedaUI.mainwindow_sections.IndexingMixin method) show_pixel_index() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.viewer.ViewerMixin method) (cosedaUI.mainwindow_sections.ViewerMixin method) show_previous_indexed_frame() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.indexing.IndexingMixin method) (cosedaUI.mainwindow_sections.IndexingMixin method) sizeHint() (cosedaUI.mainwindow.AspectRatioWidget method) start_auto_refresh() (cosedaUI.unitcell_window.UnitCellHistogramWindow method) start_coordinate_selection() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.workspace.WorkspaceMixin method) (cosedaUI.mainwindow_sections.WorkspaceMixin method) start_import() (cosedaUI.importers.import_emd_window.ImportEMDWindow method) (cosedaUI.importers.import_mrc_window.ImportMRCWindow method) (cosedaUI.importers.import_tiff_window.ImportTiffWindow method) (cosedaUI.importers.ImportEMDWindow method) (cosedaUI.importers.ImportMRCWindow method) (cosedaUI.importers.ImportTiffWindow method) start_inspect() (cosedaUI.image_tools.ImageInspector method) start_monitor() (cosedaUI.importers.import_emd_window.ImportEMDWindow method) (cosedaUI.importers.ImportEMDWindow method) start_plot() (cosedaUI.aurora_window.AuroraPlotWindow method) start_stripping() (cosedaUI.strip_file_window.StripFilesWindow method) status_update (cosedaUI.importers.import_emd_window.EMDImportThread attribute) (cosedaUI.importers.import_mrc_window.MRCImportThread attribute) (cosedaUI.importers.import_tiff_window.TiffImportThread attribute) Step1Params (class in coseda.ici.step1_hillmap_wrmsd) Step1Result (class in coseda.ici.step1_hillmap_wrmsd) Step2DxDyConfig (class in coseda.ici.step2_dxdy) stop_auto_refresh() (cosedaUI.unitcell_window.UnitCellHistogramWindow method) stop_live_preview() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.workspace.WorkspaceMixin method) (cosedaUI.mainwindow_sections.WorkspaceMixin method) stop_monitor() (cosedaUI.importers.import_emd_window.ImportEMDWindow method) (cosedaUI.importers.ImportEMDWindow method) stop_monitoring() (cosedaUI.findcenters_window.CenterFinderSettingsWindow method) (cosedaUI.refinecenters_window.CenterRefinementSettingsWindow method) stream_path (coseda.unitcell_fit.WorkspaceStreamSource attribute) strip_h5() (in module coseda.pipeline) (in module coseda.pipeline.strip_h5) strip_h5_batch() (in module coseda.pipeline) (in module coseda.pipeline.strip_h5) StripFilesWindow (class in cosedaUI.strip_file_window) StripWorker (class in cosedaUI.strip_file_window) StripWorkerBatch (class in cosedaUI.strip_file_window) stupid_tiff_folder_conversion() (in module coseda.importers.import_tiff) T tag_overlay_with_original() (in module coseda.ici.build_overlays_and_list) temp_dir (coseda.dask_client_manager.DaskClientManager attribute) text_ready (cosedaUI.ici_window.OrchestratorWorker attribute) (cosedaUI.indexintegrate_sections.helpers.OrchestratorWorker attribute) (cosedaUI.indexintegrate_sections.OrchestratorWorker attribute) textFromValue() (cosedaUI.refinecenters_window.TrimmingDoubleSpinBox method) tiff_conversion() (in module coseda.importers.import_tiff) tiff_conversion_batch() (in module coseda.importers.import_tiff) TiffImportThread (class in cosedaUI.importers.import_tiff_window) TimestampingStream (class in coseda.ici.orchestrator) translate_to_stripped_index() (in module coseda.pipeline.strip_h5) Trial (class in coseda.ici.step1_hillmap_wrmsd) (class in coseda.ici.summarize_image_run_log) TrimmingDoubleSpinBox (class in cosedaUI.refinecenters_window) U UnitCellHistogramWindow (class in cosedaUI.unitcell_window) update_cell_file_parameter() (in module coseda.unitcell_fit) update_csv_with_proposals() (in module coseda.ici.propose_next_shifts) update_detector_shifts() (in module coseda.centerfinding.findcenters_beamstop) update_final_stream_alias() (in module coseda.ici.run_contract) update_frame_from_map_click() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.workspace.WorkspaceMixin method) (cosedaUI.mainwindow_sections.WorkspaceMixin method) update_image() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.viewer.ViewerMixin method) (cosedaUI.mainwindow_sections.ViewerMixin method) update_map_thumbnail() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.viewer.ViewerMixin method) (cosedaUI.mainwindow_sections.ViewerMixin method) update_paths_old() (in module coseda.io) update_plot_viewer() (cosedaUI.findcenters_window.CenterFinderSettingsWindow method) (cosedaUI.refinecenters_window.CenterRefinementSettingsWindow method) update_preview() (cosedaUI.findcenters_window.PreviewWindow method) (cosedaUI.refinecenters_window.PreviewWindow method) update_refine_progress() (cosedaUI.refinecenters_window.CenterRefinementSettingsWindow method) update_run_list() (cosedaUI.findcenters_window.CenterFinderSettingsWindow method) (cosedaUI.peakfinder_window.PeakFinderSettingsWindow method) update_status() (cosedaUI.importers.import_emd_window.ImportEMDWindow method) (cosedaUI.importers.import_mrc_window.ImportMRCWindow method) (cosedaUI.importers.import_tiff_window.ImportTiffWindow method) (cosedaUI.importers.ImportEMDWindow method) (cosedaUI.importers.ImportMRCWindow method) (cosedaUI.importers.ImportTiffWindow method) update_workflow_buttons() (cosedaUI.mainwindow.cosedaUI method) (cosedaUI.mainwindow_sections.workspace.WorkspaceMixin method) (cosedaUI.mainwindow_sections.WorkspaceMixin method) update_workspace_refined_cell_parameter() (in module coseda.unitcell_fit) user_config_dir() (in module cosedaUI.mainwindow) V validate_geometry_for_frame() (in module coseda.detector_geometry) velox_batch() (in module coseda.importers.import_velox) velox_process() (in module coseda.importers.import_velox) velox_true_conversion() (in module coseda.importers.import_velox) velox_true_conversion_batch() (in module coseda.importers.h5convert) ViewerMixin (class in cosedaUI.mainwindow_sections) (class in cosedaUI.mainwindow_sections.viewer) W with_traceback() (coseda.centerrefinement.cancellation.RefinementCancelled method) Worker (class in cosedaUI.findcenters_window) (class in cosedaUI.refinecenters_window) WorkflowMixin (class in cosedaUI.mainwindow_sections) (class in cosedaUI.mainwindow_sections.workflow) workspace_has_refined_cell() (in module coseda.unitcell_fit) workspace_refined_cell_file_path() (in module coseda.unitcell_fit) WorkspaceMixin (class in cosedaUI.mainwindow_sections) (class in cosedaUI.mainwindow_sections.workspace) WorkspaceStreamSource (class in coseda.unitcell_fit) WorkspaceUnitCellFitWindow (class in cosedaUI.workspace_unitcell_fit_window) write() (coseda.ici.orchestrator.TimestampingStream method) (cosedaUI.ici_window.GuiStream method) (cosedaUI.indexintegrate_sections.GuiStream method) (cosedaUI.indexintegrate_sections.helpers.GuiStream method) write_all_shifts() (in module coseda.ici.build_overlays_and_list) write_atlas() (in module coseda.map.streaks) write_beam_incident_energy() (in module coseda.nexus.process) write_centerfinderdirectsettings() (in module coseda.centerfinding.findcenters_direct) write_centerfindersettings() (in module coseda.initialize) (in module coseda.initialize.settings) write_centerrefinement_direct_settings() (in module coseda.centerrefinement.refinecenters_direct) write_centerrefinementsettings() (in module coseda.initialize) (in module coseda.initialize.settings) write_cluster_ids() (in module coseda.map.mapping) write_combined_stroke_info() (in module coseda.map.findscanlines) write_detector_geometry() (in module coseda.nexus.detector) write_event_lists() (in module coseda.ici.build_overlays_and_list) write_gandalfiteratorsettings() (in module coseda.initialize) (in module coseda.initialize.settings) write_geomfile() (in module coseda.geomfile) write_h5conversionsettings() (in module coseda.initialize) (in module coseda.initialize.settings) write_icisettings() (in module coseda.initialize) (in module coseda.initialize.settings) write_index_file() (in module coseda.initialize) (in module coseda.initialize.project_files) write_log() (in module coseda.ici.propose_next_shifts) write_maxres_dataset() (in module coseda.peakfinding) (in module coseda.peakfinding.maxres) write_maxres_from_config() (in module coseda.peakfinding) (in module coseda.peakfinding.maxres) write_mergingsettings() (in module coseda.initialize) (in module coseda.initialize.settings) write_nxprocess_centerfinding() (in module coseda.nexus.process) write_nxprocess_centerrefinement() (in module coseda.nexus.process) write_nxprocess_import() (in module coseda.nexus.process) write_nxprocess_indexing() (in module coseda.nexus.process) write_nxprocess_merging() (in module coseda.nexus.process) write_nxprocess_peakfinding() (in module coseda.nexus.process) write_nxprocess_stripping() (in module coseda.nexus.process) write_overlay_mapping() (in module coseda.ici.build_overlays_and_list) write_peakfindersettings() (in module coseda.initialize) (in module coseda.initialize.settings) write_run_manifest() (in module coseda.ici.run_contract) write_shifts_mm() (in module coseda.ici.overlay_elink) write_stage_pos_to_hdf5() (in module coseda.importers.import_velox) write_stripsettings() (in module coseda.initialize) (in module coseda.initialize.settings) write_workspace_refined_cell_file() (in module coseda.unitcell_fit) write_xgandalfsettings() (in module coseda.initialize) (in module coseda.initialize.settings) wrmsd (coseda.ici.evaluate_stream.ChunkRow attribute) (coseda.ici.step1_hillmap_wrmsd.Trial attribute) (coseda.ici.summarize_image_run_log.Trial attribute) wrmsd_median_convergence() (in module coseda.ici.propose_next_shifts) wrmsd_no_improvement() (in module coseda.ici.propose_next_shifts) wrmsd_recurring_convergence() (in module coseda.ici.propose_next_shifts) wrmsd_stability() (in module coseda.ici.propose_next_shifts) X x_mm (coseda.ici.step1_hillmap_wrmsd.Trial attribute) Y y_mm (coseda.ici.step1_hillmap_wrmsd.Trial attribute)