Index

A

accept_apply() (transphire.loadwindow.DefaultSettings method) activate_tab() (transphire.plotcontainer.PlotContainer method) add_canvas() (transphire.plotwidget.PlotWidget method) add_email() (transphire.notificationcontainer.NotificationContainer method) add_exceptions() (transphire.notificationwidget.NotificationWidget method) add_save() (transphire.mountworker.MountWorker method) add_tab() (transphire.loadwindow.DefaultSettings method) (transphire.logviewerdialog.LogViewerDialog method) (transphire.tabdocker.TabDocker method)

add_tabs() (transphire.loadwindow.DefaultSettings method) add_template() (transphire.templatedialog.TemplateDialog method) add_to_layout() (transphire.plotcontainer.TwinContainer method) add_widget() (transphire.framecontainer.FrameContainer method) (transphire.loadcontentcontainer.LoadContentContainer method) append_values() (transphire.transphire_utils.DataFrame method) appendPlainText() (transphire.logviewer.LogViewer method) assign_latest() (transphire.tabdocker.TabDocker method)

C

calculate_array() (transphire.plotworker.PlotWorker method) calculate_array_now() (transphire.plotworker.PlotWorker static method) calculate_df_quota() (transphire.mountcalculator.MountCalculator method) calculate_get_quota() (transphire.mountcalculator.MountCalculator method) calculate_ssh_quota() (transphire.mountcalculator.MountCalculator method) change_color_if_true() (transphire.settingswidget.SettingsWidget method) change_info_name() (transphire.statuswidget.StatusWidget method) change_info_quota() (transphire.statuswidget.StatusWidget method) change_state() (transphire.logviewer.LogViewer method) (transphire.settingscontainer.SettingsContainer method) change_tooltip() (transphire.notificationwidget.NotificationWidget method) (transphire.settingswidget.SettingsWidget method) check_connection() (transphire.mountworker.MountWorker method) check_enable() (transphire.plotwidget.SelectWidget method) check_existence() (in module transphire.mountworker) check_instance() (in module transphire.transphire_utils) check_modified_widgets() (transphire.loadwindow.DefaultSettings method) choose_template() (transphire.templatedialog.TemplateDialog method) clear_canvas() (transphire.plotwidget.PlotWidget method) clear_combo() (transphire.notificationwidget.NotificationWidget method) clear_tabs() (transphire.loadwindow.DefaultSettings method) closeEvent() (transphire.loadwindow.DefaultSettings method) combine_ctf_outputs() (in module transphire.transphire_ctf) contrast_to_shift() (in module transphire.transphire_ctf)

copy() (in module transphire.transphire_utils) copy_from_template() (transphire.loadcontentcontainer.LoadContentContainer method) copy_template() (transphire.templatedialog.TemplateDialog method) copytree() (in module transphire.transphire_utils) count() (transphire.tabdocker.TabDocker method) create_box() (in module transphire.transphire_picking) create_circle() (in module transphire.transphire_picking) create_cryolo_v1_0_4_command() (in module transphire.transphire_picking) create_cryolo_v1_1_0_command() (in module transphire.transphire_picking) create_cryolo_v1_4_1_command() (in module transphire.transphire_picking) create_cter_1_0_command() (in module transphire.transphire_ctf) create_cter_1_3_command() (in module transphire.transphire_ctf) create_ctffind_4_v4_1_13_command() (in module transphire.transphire_ctf) create_ctffind_4_v4_1_8_command() (in module transphire.transphire_ctf) create_eval_command() (in module transphire.transphire_train2d) create_export_data() (in module transphire.transphire_ctf) create_filter_command() (in module transphire.transphire_picking) create_gctf_v1_06_command() (in module transphire.transphire_ctf) create_initial_tabs() (transphire.loadwindow.DefaultSettings method) create_log() (in module transphire.transphire_utils) create_restack_command() (in module transphire.transphire_train2d) create_substack_command() (in module transphire.transphire_train2d) create_train_command() (in module transphire.transphire_train2d) currentIndex() (transphire.tabdocker.TabDocker method)

D

DataFrame (class in transphire.transphire_utils) default_auto_sphire_v1_3() (in module transphire.transphire_content) default_cinderella_v0_3_1() (in module transphire.transphire_content) default_compress_command_line() (in module transphire.transphire_content) default_copy() (in module transphire.transphire_content) default_cryolo_train_v1_5_4() (in module transphire.transphire_content) default_cryolo_train_v1_5_8() (in module transphire.transphire_content) default_cryolo_train_v1_7_4() (in module transphire.transphire_content) default_cryolo_v1_0_4() (in module transphire.transphire_content) default_cryolo_v1_1_0() (in module transphire.transphire_content) default_cryolo_v1_2_1() (in module transphire.transphire_content) default_cryolo_v1_4_1() (in module transphire.transphire_content) default_cryolo_v1_5_8() (in module transphire.transphire_content) default_cter_v1_0() (in module transphire.transphire_content) default_ctffind_4_v4_1_8() (in module transphire.transphire_content) default_font() (in module transphire.transphire_content) default_gctf_v1_06() (in module transphire.transphire_content) default_gctf_v1_18() (in module transphire.transphire_content) default_general() (in module transphire.transphire_content) default_global() (in module transphire.transphire_content)

default_input() (in module transphire.transphire_content) default_isac2_1_2() (in module transphire.transphire_content) default_motion_cor_2_v1_0_0() (in module transphire.transphire_content) default_motion_cor_2_v1_0_5() (in module transphire.transphire_content) default_motion_cor_2_v1_1_0() (in module transphire.transphire_content) default_motion_cor_2_v1_3_0() (in module transphire.transphire_content) default_mount() (in module transphire.transphire_content) default_notification() (in module transphire.transphire_content) default_notification_widget() (in module transphire.transphire_content) default_others() (in module transphire.transphire_content) default_path() (in module transphire.transphire_content) default_pipeline() (in module transphire.transphire_content) default_unblur_v1_0_0() (in module transphire.transphire_content) default_window_1_2() (in module transphire.transphire_content) DefaultSettings (class in transphire.loadwindow) delete (transphire.framewidget.FrameWidget attribute) (transphire.loadcontent.LoadContent attribute) do_data_reset() (transphire.plotwidget.PlotWidget method) dummy() (in module transphire.transphire_import) (in module transphire.transphire_plot)

E

EmailDialog (class in transphire.emaildialog) emit_global() (transphire.settingscontainer.SettingsContainer method) emit_signals() (transphire.settingscontainer.SettingsContainer method) enable() (transphire.framecontainer.FrameContainer method) (transphire.mountcontainer.MountContainer method) (transphire.notificationcontainer.NotificationContainer method) (transphire.plotcontainer.PlotContainer method) (transphire.settingscontainer.SettingsContainer method)

enable_tab() (transphire.tabdocker.TabDocker method) enlarge() (transphire.settingswidget.SettingsWidget method) eventFilter() (transphire.plotcontainer.PlotContainer method)

F

fill_default_dict() (transphire.loadwindow.DefaultSettings method) fill_quota_project_and_scratch() (transphire.mountworker.MountWorker method) filter_combo() (transphire.plotwidget.SelectWidget method) find_best_match() (in module transphire.transphire_utils) find_latest_version() (in module transphire.transphire_utils)

find_logfiles() (in module transphire.transphire_ctf) (in module transphire.transphire_picking) force_update() (transphire.plotwidget.PlotWidget method) FrameContainer (class in transphire.framecontainer) FrameWidget (class in transphire.framewidget)

G

get_apply() (transphire.loadwindow.DefaultSettings method) get_color() (in module transphire.transphire_utils) get_combo_entries() (transphire.settingswidget.SettingsWidget method) get_constant_value() (in module transphire.transphire_ctf) get_content_default() (transphire.loadwindow.DefaultSettings static method) get_content_gui() (in module transphire.transphire_utils) get_ctf_command() (in module transphire.transphire_ctf) get_current_global() (transphire.settingswidget.SettingsWidget method) get_df() (transphire.transphire_utils.DataFrame method) get_dtype_dict() (in module transphire.transphire_import) get_dtype_import_dict() (in module transphire.transphire_import) get_email() (transphire.emaildialog.EmailDialog method) get_exclude_set_path() (in module transphire.transphire_utils) get_folder_size() (transphire.mountcalculator.MountCalculator method) get_function_dict() (in module transphire.transphire_utils) get_header() (in module transphire.transphire_import) get_index_where() (transphire.transphire_utils.DataFrame method) get_indicator() (transphire.logviewer.LogViewer method) get_input_names() (transphire.settingscontainer.SettingsContainer method) get_key_names() (in module transphire.transphire_utils) get_mic_number() (in module transphire.transphire_plot) get_name() (in module transphire.transphire_utils) (transphire.emaildialog.EmailDialog method) get_picking_command() (in module transphire.transphire_picking) get_quota_quota_command() (transphire.mountcalculator.MountCalculator static method)

get_relion_dict() (in module transphire.transphire_import) get_relion_header() (in module transphire.transphire_ctf) get_restart_dict() (transphire.inputbox.InputBox method) get_settings() (transphire.framecontainer.FrameContainer method) (transphire.framewidget.FrameWidget method) (transphire.loadcontent.LoadContent method) (transphire.loadcontentcontainer.LoadContentContainer method) (transphire.mountcontainer.MountContainer method) (transphire.mountwidget.MountWidget method) (transphire.notificationcontainer.NotificationContainer method) (transphire.notificationwidget.NotificationWidget method) (transphire.settingscontainer.SettingsContainer method) (transphire.settingswidget.SettingsWidget method) get_settings_tab() (transphire.loadcontentcontainer.LoadContentContainer method) get_settings_widget() (transphire.loadcontentcontainer.LoadContentContainer method) get_ssh_quota() (transphire.mountcalculator.MountCalculator method) get_style() (in module transphire.transphire_utils) get_telegram_messages() (transphire.notificationcontainer.NotificationContainer method) get_telegram_user() (transphire.notificationcontainer.NotificationContainer method) get_transphire_dict() (in module transphire.transphire_import) get_unique_types() (in module transphire.transphire_utils) get_value() (transphire.plotwidget.SelectWidget method) get_values() (transphire.plotwidget.TrimWidget method) (transphire.transphire_utils.DataFrame method) getText() (transphire.inputbox.InputBox method)

H

handle_change() (transphire.plotwidget.SelectWidget method) handle_check() (transphire.inputbox.InputBox method) handle_show() (transphire.plotcontainer.TwinContainer method)

hide_marker() (transphire.plotwidget.PlotWidget method) hide_show_widget() (transphire.separator.Separator method) hide_twin() (transphire.plotwidget.PlotWidget method) high_res() (transphire.plotwidget.PlotWidget static method)

I

import_auto_sphire_v1_3() (in module transphire.transphire_import) import_cinderella_v0_3_1() (in module transphire.transphire_import) import_cryolo_v1_0_4() (in module transphire.transphire_import) import_cryolo_v1_2_2() (in module transphire.transphire_import) import_cter_v1_0() (in module transphire.transphire_import) import_ctffind_v4_1_8() (in module transphire.transphire_import) import_gctf_v1_06() (in module transphire.transphire_import) import_isac_v1_2() (in module transphire.transphire_import)

import_motion_cor_2_v1_0_0() (in module transphire.transphire_import) import_unblur_v1_0_0() (in module transphire.transphire_import) import_window_v1_2() (in module transphire.transphire_import) increment_indicator() (transphire.logviewer.LogViewer method) indexOf() (transphire.tabdocker.TabDocker method) InputBox (class in transphire.inputbox) is_higher_version() (in module transphire.transphire_utils) is_in_content() (transphire.loadwindow.DefaultSettings method)

L

latest_active (transphire.tabdocker.TabDocker attribute) load_df() (transphire.transphire_utils.DataFrame method) load_save() (transphire.mountworker.MountWorker method) load_template() (transphire.loadwindow.DefaultSettings method) LoadContent (class in transphire.loadcontent)

LoadContentContainer (class in transphire.loadcontentcontainer) LogViewer (class in transphire.logviewer) LogViewerDialog (class in transphire.logviewerdialog) look_and_feel() (in module transphire.transphire_utils) look_and_feel_small() (in module transphire.transphire_utils)

M

message() (in module transphire.transphire_utils) MessageBox (class in transphire.messagebox) mkdir_p() (in module transphire.transphire_utils) mount() (transphire.mountwidget.MountWidget method) (transphire.mountworker.MountWorker method) mount_hdd() (transphire.mountworker.MountWorker method) MountCalculator (class in transphire.mountcalculator)

MountContainer (class in transphire.mountcontainer) MountWidget (class in transphire.mountwidget) MountWorker (class in transphire.mountworker) mouse_twin_event() (transphire.plotcontainer.TwinContainer method) MplCanvas (class in transphire.plotwidget) MplCanvasWidget (class in transphire.plotwidget) my_click_event() (transphire.logviewer.LogViewer method) MyTabBar (class in transphire.tabdocker)

N

normalize_image() (in module transphire.transphire_utils)

NotificationContainer (class in transphire.notificationcontainer) NotificationWidget (class in transphire.notificationwidget)

O

order_tabs() (transphire.tabdocker.TabDocker method)

P

paintEvent() (transphire.tabdocker.MyTabBar method) PasswordDialog (class in transphire.passworddialog) PlotContainer (class in transphire.plotcontainer)

PlotWidget (class in transphire.plotwidget) PlotWorker (class in transphire.plotworker) prepare_axes() (transphire.plotwidget.PlotWidget method) prepare_send_adjust() (transphire.settingscontainer.SettingsContainer method)

Q

question() (in module transphire.transphire_utils)

R

rebin() (in module transphire.transphire_utils) recursive_clear() (transphire.loadwindow.DefaultSettings method) recursive_file_search() (in module transphire.transphire_ctf) recursive_search() (transphire.settingscontainer.SettingsContainer static method) reduce_copy_entries() (in module transphire.transphire_utils) reduce_path_widget() (in module transphire.transphire_utils) reduce_programs() (in module transphire.transphire_utils) refresh_quota() (transphire.mountworker.MountWorker method) (transphire.statuscontainer.StatusContainer method)

remove_template() (transphire.templatedialog.TemplateDialog method) remove_widget() (transphire.loadcontentcontainer.LoadContentContainer method) removeTab() (transphire.tabdocker.TabDocker method) rerun_function_in_case_of_error() (in module transphire.transphire_utils) reset_list() (transphire.plotworker.PlotWorker method) reset_plain_text() (transphire.logviewer.LogViewer method) reset_plot() (transphire.plotcontainer.PlotContainer method) reset_values() (transphire.plotwidget.SelectWidget method) (transphire.plotwidget.TrimWidget method)

S

save_df() (transphire.transphire_utils.DataFrame method) save_settings() (transphire.loadcontentcontainer.LoadContentContainer method) search_for_projects() (transphire.settingscontainer.SettingsContainer method) select_tab() (transphire.plotcontainer.PlotContainer method) SelectWidget (class in transphire.plotwidget) send_data() (transphire.plotworker.PlotWorker method) send_notification() (transphire.notificationcontainer.NotificationContainer method) send_to_user() (transphire.notificationcontainer.NotificationContainer method) Separator (class in transphire.separator) set_current_folder() (transphire.mountwidget.MountWidget method) set_current_image_name() (transphire.plotwidget.PlotWidget method) set_design() (transphire.settingscontainer.SettingsContainer method) set_df() (transphire.transphire_utils.DataFrame method) set_floating() (transphire.plotcontainer.PlotContainer method) set_global() (transphire.settingscontainer.SettingsContainer method) set_new_model() (transphire.settingscontainer.SettingsContainer method) set_project_path() (transphire.logviewer.LogViewer method) set_settings() (transphire.framecontainer.FrameContainer method) (transphire.loadcontent.LoadContent method) (transphire.loadcontentcontainer.LoadContentContainer method) (transphire.mountworker.MountWorker method) (transphire.notificationcontainer.NotificationContainer method) (transphire.notificationwidget.NotificationWidget method) (transphire.plotwidget.PlotWidget method) (transphire.plotworker.PlotWorker method) (transphire.settingscontainer.SettingsContainer method) (transphire.settingswidget.SettingsWidget method) set_state() (transphire.plotwidget.TrimWidget method) set_thread_object() (transphire.mountwidget.MountWidget method) set_threadlist() (transphire.mountcontainer.MountContainer method) set_type() (transphire.inputbox.InputBox method) set_values() (transphire.plotwidget.SelectWidget method) (transphire.plotwidget.TrimWidget method) (transphire.transphire_utils.DataFrame method) set_visibility() (transphire.plotcontainer.PlotContainer method) setCurrentIndex() (transphire.tabdocker.TabDocker method) setCurrentWidget() (transphire.tabdocker.TabDocker method) setDefault() (transphire.inputbox.InputBox method) (transphire.messagebox.MessageBox method) setMovable() (transphire.tabdocker.TabDocker method) setTabEnabled() (transphire.tabdocker.TabDocker method) setTabPosition() (transphire.tabdocker.TabDocker method) setTabText() (transphire.tabdocker.TabDocker method) setText() (transphire.inputbox.InputBox method) (transphire.messagebox.MessageBox method) SettingsContainer (class in transphire.settingscontainer) SettingsWidget (class in transphire.settingswidget)

setup_values() (transphire.plotwidget.PlotWidget method) shift_to_contrast() (in module transphire.transphire_ctf) sig_add_save (transphire.mountworker.MountWorker attribute) sig_adjust_tab (transphire.settingscontainer.SettingsContainer attribute) sig_calculate (transphire.plotworker.PlotWorker attribute) sig_calculate_df_quota (transphire.mountworker.MountWorker attribute) sig_calculate_get_quota (transphire.mountworker.MountWorker attribute) sig_calculate_ssh_quota (transphire.mountworker.MountWorker attribute) sig_change_info_name (transphire.statuswidget.StatusWidget attribute) sig_change_info_quota (transphire.statuswidget.StatusWidget attribute) sig_change_use_movie (transphire.settingscontainer.SettingsContainer attribute) sig_data (transphire.plotworker.PlotWorker attribute) sig_error (transphire.mountworker.MountWorker attribute) sig_finished (transphire.mountcalculator.MountCalculator attribute) sig_hide (transphire.plotwidget.TrimWidget attribute) (transphire.plotwidget.ViewWidget attribute) sig_index_changed (transphire.settingswidget.SettingsWidget attribute) sig_info (transphire.mountworker.MountWorker attribute) sig_load_save (transphire.mountworker.MountWorker attribute) sig_mount (transphire.mountworker.MountWorker attribute) sig_mount_hdd (transphire.mountworker.MountWorker attribute) sig_new_round (transphire.plotworker.PlotWorker attribute) sig_notification (transphire.mountworker.MountWorker attribute) sig_quota (transphire.mountworker.MountWorker attribute) sig_refresh (transphire.mountworker.MountWorker attribute) sig_refresh_quota (transphire.statuscontainer.StatusContainer attribute) sig_reset (transphire.plotworker.PlotWorker attribute) sig_reset_list (transphire.plotworker.PlotWorker attribute) sig_set_folder (transphire.mountworker.MountWorker attribute) sig_set_settings (transphire.mountworker.MountWorker attribute) sig_set_state (transphire.plotwidget.TrimWidget attribute) sig_set_visual (transphire.plotworker.PlotWorker attribute) sig_start_plot (transphire.tabdocker.TabDocker attribute) sig_stop (transphire.notificationcontainer.NotificationContainer attribute) sig_success (transphire.mountworker.MountWorker attribute) sig_twin (transphire.plotwidget.MplCanvas attribute) sig_umount (transphire.mountworker.MountWorker attribute) sig_update (transphire.plotwidget.SelectWidget attribute) (transphire.plotwidget.TrimWidget attribute) sig_visible (transphire.plotworker.PlotWorker attribute) split_maximum() (in module transphire.transphire_utils) start_plotting() (transphire.plotwidget.PlotWidget method) StatusContainer (class in transphire.statuscontainer) StatusWidget (class in transphire.statuswidget) submit_text() (transphire.logviewer.LogViewer method) symlink_rel() (in module transphire.transphire_utils) synchronize_tabs() (transphire.plotcontainer.PlotContainer method)

T

TabDocker (class in transphire.tabdocker) tabSizeHint() (transphire.tabdocker.MyTabBar method) tabText() (transphire.tabdocker.TabDocker method) TemplateDialog (class in transphire.templatedialog) thread_safe() (in module transphire.transphire_utils) to_partres_file() (in module transphire.transphire_ctf) to_star_file() (in module transphire.transphire_ctf) tooltip_style() (in module transphire.transphire_utils) transphire (module) transphire.emaildialog (module) transphire.framecontainer (module) transphire.framewidget (module) transphire.inputbox (module) transphire.loadcontent (module) transphire.loadcontentcontainer (module) transphire.loadwindow (module) transphire.logviewer (module) transphire.logviewerdialog (module) transphire.messagebox (module) transphire.mountcalculator (module) transphire.mountcontainer (module) transphire.mountwidget (module) transphire.mountworker (module)

transphire.notificationcontainer (module) transphire.notificationwidget (module) transphire.passworddialog (module) transphire.plotcontainer (module) transphire.plotwidget (module) transphire.plotworker (module) transphire.separator (module) transphire.settingscontainer (module) transphire.settingswidget (module) transphire.statuscontainer (module) transphire.statuswidget (module) transphire.support_scripts (module) transphire.tabdocker (module) transphire.templatedialog (module) transphire.transphire_content (module) transphire.transphire_ctf (module) transphire.transphire_import (module) transphire.transphire_picking (module) transphire.transphire_plot (module) transphire.transphire_train2d (module) transphire.transphire_utils (module) TrimWidget (class in transphire.plotwidget) TwinContainer (class in transphire.plotcontainer)

U

umount() (transphire.mountwidget.MountWidget method) (transphire.mountworker.MountWorker method) update() (transphire.notificationcontainer.NotificationContainer method) update_batch() (in module transphire.transphire_plot) update_combo() (transphire.notificationwidget.NotificationWidget method) update_cryolo_v1_0_4() (in module transphire.transphire_plot) update_ctf() (in module transphire.transphire_plot) update_data() (transphire.plotwidget.PlotWidget method) update_email() (transphire.notificationcontainer.NotificationContainer method) update_figure() (transphire.plotcontainer.PlotContainer method) (transphire.plotwidget.PlotWidget method) update_global() (transphire.settingscontainer.SettingsContainer method)

update_helpers() (transphire.plotwidget.PlotWidget method) update_histogram() (transphire.plotwidget.PlotWidget method) update_image() (transphire.plotwidget.PlotWidget method) update_image_plot() (transphire.plotwidget.PlotWidget method) update_label() (transphire.plotwidget.ViewWidget method) update_labels() (transphire.plotwidget.MplCanvasWidget method) update_micrograph() (in module transphire.transphire_plot) update_motion() (in module transphire.transphire_plot) update_plain_text() (transphire.logviewer.LogViewer method) update_telegram() (transphire.notificationcontainer.NotificationContainer method) update_trim() (transphire.plotwidget.PlotWidget method) update_values() (transphire.plotwidget.PlotWidget method)

V

value_in_column() (transphire.transphire_utils.DataFrame method)

ViewWidget (class in transphire.plotwidget)

W

widget() (transphire.tabdocker.TabDocker method)