TileServer¶

tiatoolbox . visualization . tileserver . TileServer

class TileServer(title, layers, renderer=None)[source]¶

A Flask app to display Zoomify tiles as a slippery map.

Parameters:

title (str) – The title of the tile server, displayed in the browser as the page title.
layers (Dict[str, WSIReader | str] | List[WSIReader | str]) – A dictionary mapping layer names to image paths, annotation paths, or WSIReader objects to display. The dictionary should have a ‘slide’ key which is the base slide for the visualization. May also be a list, in which case generic names ‘slide’, ‘layer-1’, ‘layer-2’ etc. will be used. First entry in list will be assumed to be the base slide. If a layer is a single-channel low-res overlay, it will be colourized using the ‘viridis’ colourmap.
renderer (AnnotationRenderer | None)

Examples

>>> from tiatoolbox.wsicore.wsireader import WSIReader
>>> from tiatoolbox.visualization.tileserver import TileServer
>>> wsi = WSIReader.open("CMU-1.svs")
>>> app = TileServer(
...     title="Testing TileServer",
...     layers={
...         "My SVS": wsi,
...     },
... )
>>> app.run()

Initialize TileServer.

Methods

`change_mapper`	Change the colour mapper for the overlay.
`change_overlay`	Change the overlay.
`change_prop`	Change the property to colour annotations by.
`change_secondary_cmap`	Change the type-specific colour mapper for the overlay.
`change_slide`	Change the slide.
`commit_db`	Commit changes to the current store.
`decode_safe_name`	Decode a URL-safe name.
`get_ann_layer`	Get the annotation layer for a session_id.
`get_annotations`	Get the annotations in the specified bounds.
`get_color_prop`	Get the property used to color annotations from renderer.
`get_mapper`	Get the mapper used to color annotations from renderer.
`get_overlay`	Get the overlay info.
`get_properties`	Get all the properties of the annotations in the store.
`get_property_values`	Get all the values of a property in the store.
`get_renderer`	Get the requested property from the renderer.
`get_secondary_cmap`	Get the secondary cmap from the renderer.
`get_slide`	Get the slide metadata.
`index`	Serve the index page.
`load_annotations`	Load annotations from a dat file.
`prop_range`	Set the range which the color mapper will map to.
`reset`	Reset the tileserver.
`session_id`	Set up a new session.
`shutdown`	Shutdown the tileserver.
`tap_query`	Query for annotations at a point.
`update_renderer`	Update a property in the renderer.
`update_types`	Get the available types from the store.
`zoomify`	Serve a Zoomify tile for a particular layer.

Attributes

`cli`	The Click command group for registering CLI commands for this object.
`instance_path`	Holds the path to the instance folder.
`config`	The configuration dictionary as `Config`.
`aborter`	An instance of `aborter_class` created by `make_aborter()`.
`json`	Provides access to JSON methods.
`url_build_error_handlers`	A list of functions that are called by `handle_url_build_error()` when `url_for()` raises a `BuildError`.
`teardown_appcontext_funcs`	A list of functions that are called when the application context is destroyed.
`shell_context_processors`	A list of shell context processor functions that should be run when a shell context is created.
`blueprints`	Maps registered blueprint names to blueprint objects.
`extensions`	a place where extensions can store application specific state.
`url_map`	The `Map` for this instance. You can use this to change the routing converters after the class was created but before any routes are connected. Example::.
`import_name`	The name of the package or module that this object belongs to.
`template_folder`	The path to the templates folder, relative to `root_path`, to add to the template loader.
`root_path`	Absolute path to the package on the filesystem.
`view_functions`	A dictionary mapping endpoint names to view functions.
`error_handler_spec`	A data structure of registered error handlers, in the format `{scope: {code: {class: handler}}}`.
`before_request_funcs`	A data structure of functions to call at the beginning of each request, in the format `{scope: [functions]}`.
`after_request_funcs`	A data structure of functions to call at the end of each request, in the format `{scope: [functions]}`.
`teardown_request_funcs`	A data structure of functions to call at the end of each request even if an exception is raised, in the format `{scope: [functions]}`.
`template_context_processors`	A data structure of functions to call to pass extra context values when rendering templates, in the format `{scope: [functions]}`.
`url_value_preprocessors`	A data structure of functions to call to modify the keyword arguments passed to the view function, in the format `{scope: [functions]}`.
`url_default_functions`	A data structure of functions to call to modify the keyword arguments when generating URLs, in the format `{scope: [functions]}`.

change_mapper()[source]¶

Change the colour mapper for the overlay.

Parameters:: self (TileServer)
Return type:: str

change_overlay()[source]¶

Change the overlay.

If the path points to some annotations, the current overlay is replaced with the new one. If the path points to an image, it is added as a new layer.

Returns:: A jsonified list of types.
Return type:: str
Parameters:: self (TileServer)

change_prop()[source]¶

Change the property to colour annotations by.

Parameters:: self (TileServer)
Return type:: str

change_secondary_cmap()[source]¶

Change the type-specific colour mapper for the overlay.

Parameters:: self (TileServer)
Return type:: str

change_slide()[source]¶

Change the slide.

Parameters:: self (TileServer)
Return type:: str

commit_db()[source]¶

Commit changes to the current store.

If the store is not already associated with a .db file, the save_path is used to create a new .db file.

Parameters:: self (TileServer)
Return type:: str

static decode_safe_name(name)[source]¶

Decode a URL-safe name.

Parameters:: name (str)
Return type:: Path

get_ann_layer(session_id)[source]¶

Get the annotation layer for a session_id.

Parameters:

self (TileServer)
session_id (str)

Return type:

AnnotationTileGenerator | ValueError

get_annotations()[source]¶

Get the annotations in the specified bounds.

Parameters:: self (TileServer)
Return type:: Response

get_color_prop()[source]¶

Get the property used to color annotations from renderer.

Parameters:: self (TileServer)
Return type:: Response

get_mapper()[source]¶

Get the mapper used to color annotations from renderer.

Parameters:: self (TileServer)
Return type:: Response

get_overlay()[source]¶

Get the overlay info.

Parameters:: self (TileServer)
Return type:: Response

get_properties(ann_type)[source]¶

Get all the properties of the annotations in the store.

Parameters:

ann_type (str) – The type of annotations to get the properties for.
self (TileServer)

Returns:

A jsonified list of the properties.

Return type:

str

get_property_values(prop, ann_type)[source]¶

Get all the values of a property in the store.

Parameters:

prop (str) – The property to get the values of.
ann_type (str) – The type of annotations to get the values for.
self (TileServer)

Returns:

A jsonified list of the values of the property.

Return type:

str

get_renderer(prop)[source]¶

Get the requested property from the renderer.

Parameters:

self (TileServer)
prop (str)

Return type:

Response

get_secondary_cmap()[source]¶

Get the secondary cmap from the renderer.

Parameters:: self (TileServer)
Return type:: Response

get_slide()[source]¶

Get the slide metadata.

Parameters:: self (TileServer)
Return type:: Response

index()[source]¶

Serve the index page.

Returns:: The index page.
Return type:: flask.Response
Parameters:: self (TileServer)

load_annotations()[source]¶

Load annotations from a dat file.

Adds to an existing store if one is already present, otherwise creates a new store.

Returns:: A jsonified list of types.
Return type:: str
Parameters:: self (TileServer)

prop_range()[source]¶

Set the range which the color mapper will map to.

It will create an appropriate function to map the range to the range [0, 1], and set the renderers score_fn to this function.

Parameters:: self (TileServer)
Return type:: str

reset(session_id)[source]¶

Reset the tileserver.

Parameters:

self (TileServer)
session_id (str)

Return type:

str

session_id()[source]¶

Set up a new session.

Parameters:: self (TileServer)
Return type:: Response

static shutdown()[source]¶

Shutdown the tileserver.

Return type:: None

tap_query(x, y)[source]¶

Query for annotations at a point.

Parameters:

x (float) – The x coordinate.
y (float) – The y coordinate.
self (TileServer)

Returns:

The jsonified dict of the properties of the smallest annotation returned from the query at the point.

Return type:

Response

update_renderer(prop)[source]¶

Update a property in the renderer.

Parameters:

prop (str) – The property to update.
self (TileServer)

Return type:

str

static update_types(sq)[source]¶

Get the available types from the store.

Parameters:: sq (SQLiteStore)
Return type:: tuple

zoomify(layer, session_id, tile_group, z, x, y, res)[source]¶

Serve a Zoomify tile for a particular layer.

Note that this should not be called directly, but will be called automatically by the Flask framework when a client requests a tile at the registered URL.

Parameters:

layer (str) – The layer name.
session_id (str) – Session ID. Unique ID to disambiguate requests from different sessions.
tile_group (int) – The tile group. Currently unused.
z (int) – The zoom level.
x (int) – The x coordinate.
y (int) – The y coordinate.
res (int) – Resolution to save the tiles at. Helps to specify high resolution tiles. Valid options are 1 and 2.
self (TileServer)

Returns:

The tile image response.

Return type:

flask.Response