neurocarto.main_app

class neurocarto.main_app.CartoApp

Application of neural probe channelmap editor.

The layout of this application is split into:

left: channelmap manipulating button groups.
center: figure that contains probe/electrodes, image and curves.
right: controls of image, curves that shown in center panel.

user_views_config: dict[str, Any] = {}: user view configuration

right_panel_views_config: dict[str, Any] = {}: view configuration, channelmap depended

__init__(config, *, logger='neurocarto.editor')

Parameters:

config (CartoConfig)
logger (str)

probe: ProbeDesp[M, Any]: probe describer

property title: str: Application title (shown in web page title)

current_resource_root()

get current resource root.

Returns:: path
See:: channelmap_root
Return type:: Path

change_resource_root(root)

change resource root.

Parameters:: root (str | Path) – path
See:: channelmap_root

load_user_config(*, reset=False)

load user config.

Parameters:: reset – reset user config. Otherwise, just update dict.
Returns:
See:: load_user_config()
Return type:: dict[str, Any]

save_user_config(direct=False)

save user config.

Parameters:: direct – Do not update configurations from GlobalStateView.
See:: save_user_config()

get_editor_userconfig()

get editor config from user config.

Returns:
Return type:: CartoUserConfig

list_chmap_files(recursive=True)

List channelmap files under chmap-dir (-C, --chmap-dir).

Parameters:: recursive (bool) – recursive search the files in folders.
Returns:: list of files
See:: list_channelmap_files()
Return type:: list[Path]

get_chmap_file(name)

Get channelmap file path.

Parameters:: name (str) – filename. it should be the filename under chmap-dir. Otherwise, it needs to contain ‘/’ to load from/save into other place.
Returns:: saving path.
See:: {files#get_channelmap_file()}
Return type:: Path

load_chmap(name)

Load channelmap from file with name.

Parameters:: name (str | Path) – filename. See get_chmap_file() for more details.
Returns:: channelmap instance.
Return type:: M

save_chmap(name, chmap)

Save channelmap into file.

Parameters:

name (str) – filename. See get_chmap_file() for more details.
chmap (M) – channelmap instance.

Returns:

saved path.

Return type:

Path

get_blueprint_file(chmap)

Get corresponded blueprint file from channelmap path.

A blueprint is a numpy array, and saved with a suffix ‘.blueprint.npy’. Sometimes, we encode the channelmap type code inside, e.g. ‘.CODE.blueprint.npy’, when the blueprint file does not have the corresponding channelmap file.

Parameters:: chmap (str | Path) – filename. See get_chmap_file() for more details.
Returns:: saving path.
See:: get_blueprint_file()
Return type:: Path

load_blueprint(chmap)

Load channelmap chmap corresponded blueprint.

Parameters:: chmap (str | Path) – filename. See get_blueprint_file() for more details.
Returns:: True on success.
Return type:: bool

save_blueprint(chmap)

Save channelmap chmap corresponded blueprint.

Parameters:: chmap (str | Path) – filename. See get_blueprint_file() for more details.
Returns:: saving path. None on failure.
Return type:: Path | None

get_view_config_file(chmap)

Get view components’ configurations saving path.

Parameters:: chmap (str | Path) – filename. See get_chmap_file() for more details.
Returns:: saving path.
See:: get_view_config_file()
Return type:: Path

load_view_config(chmap, *, reset=False, error=False)

Load view components’ configurations.

Parameters:

chmap (str | Path) – filename. See get_view_config_file() for more details.
reset – reset right_view_config or update.
error – raise FileNotFoundError if chmap does not exist, instead of warning.

Returns:

configuration dict {type_name: Any}.

Return type:

dict[str, Any]

save_view_config(chmap, *, direct=False)

Save view components’ configurations.

Parameters:

chmap (str | Path) – filename. See get_view_config_file() for more details.
direct – Do not update configurations from view components.

probe_fig: figure

probe_view: ProbeView

right_panel_views: list[ViewBase]

input_imro: Select

output_imro: AutocompleteInput

message_area: TextAreaInput

auto_btn: Toggle

index(): Web-page document content

install_right_panel_views(config)

Parameters:: config (CartoConfig)
Returns:: list of item that recognised by init_view()
Return type:: list

start(): Invoked when session set

cleanup(context)

Invoked when session destroyed

Parameters:: context (SessionContext)

on_new(e)

callback function on new a probe instance.

Parameters:: e (int | str | MenuItemClick) – probe code, name. It could be an event but for internal using.

on_load(): callback function on loading a channelmap file.

load_file(name)

load a channelmap file.

Parameters:: name (str | Path) – channelmap filename or filepath. Could be a view config json file (*.config.json).

reload_input_file_list(preselect=None)

reload the channelmap file list and update the UI components, including input_imro’s options list and selected filename, and output_imro’s completion list.

Parameters:: preselect (str | None) – selected filename

on_save()

callback function on saving a channelmap file.

This saving also save accompanying files with the channelmap file, like blueprint file and view configuration file.

Note

Only valid channelmap can be saved, as well as its accompanying files.

The user config “always_save_blueprint_file” allow the blueprint file can be saved even if the channelmap is invalid.

on_state_change(state)

callback function on any state button is pressed.

This callback changes the state of captured electrodes.

Parameters:: state (int) – state code

on_category_change(category)

callback function on any category button is pressed.

This callback changes the category of captured electrodes.

Parameters:: category (int) – category code

on_probe_update(): callback function to notify the DynamicView that the probe has updated.

on_autoupdate(active)

callback function on the state of the auto_btn changed.

Parameters:: active (bool) – Does the auto trigger enable?

on_refresh(): callback function to refresh the electrode selection.

log_message(*message, reset=False)

print messages at log area.

Parameters:

message – messages.
reset – reset text area.

log_clear(): Clear log text area.

neurocarto.main_app.main(config=None)

Start application.

Parameters:: config (CartoConfig | None)

class neurocarto.main_app.CartoUserConfig

User config for CartoApp.

All key are optional.

{
  "CartoApp": {
    "theme": "",
    "views": [],
    "history": false,
    "overwrite_chmap_file": false,
    "always_save_blueprint_file": false,
    "selected_as_pre_selected": false,
  }
}

theme: str | dict[str, Any] | None: Bokeh theme. see https://docs.bokeh.org/en/latest/docs/reference/themes.html#theme

views: list[str]: Extra {ViewBase} list

history: bool: Enable History. Default False

overwrite_chmap_file: bool: overwrite channelmap file by default. Default False

always_save_blueprint_file: bool: always save the blueprint file even if the channelmap still invalid.

selected_as_pre_selected: bool: set selected electrode as pre-select category when constructing on blank (or only preselect category) blueprint. Default False.