fusion_tools.visualization package

fusion_tools.visualization.components module

class fusion_tools.visualization.components.Visualization(local_slides: list | str | None = None, local_annotations: list | dict | None = None, slide_metadata: list | dict | None = None, tileservers: list | TileServer | None = None, components: list | dict = [], header: list | None = None, app_options: dict = {}, linkage: list | str = 'row')

Bases: object

General holder class used for initialization. Components added after initialization. To initialize a new visualization session, you can use the following syntax:

# This is for a slide stored on the same computer you're running the fusion-tools instance from.
local_slide = ['/path/to/slide.tif']
annotations = ['/path/to/annotations.json']
components = [
    [
        SlideMap()
    ],
    [
        [
            OverlayOptions(),
            PropertyViewer()
        ]
    ]
]
vis_session = Visualization(
    local_slides = local_slide,
    local_annotations = local_annotations,
    components = components
)
vis_session.start()

check_for_uploader(components)

gen_header_components()

gen_layout()

Generating Visualization layout

Returns:: Total layout containing embedded components
Return type:: dmc.MantineProvider

get_callbacks()

get_layout_children()

Generating layout of embedded components from structure of components list

Returns:: List of dbc.Row(dbc.Col(dbc.Tabs())) components
Return type:: list

initialize_stores()

open_header(clicked, is_open)

open_header_component(clicked, session_data)

open_navbar(clicked, is_open)

start(): Starting visualization session based on provided app_options

update_page(pathname, path_button, session_data)

Updating page in multi-page application

Parameters:: pathname (str) – Pathname or suffix of current url which is a key to the page name

update_page_layout(page_components_list: list, use_prefix: bool, session_data: list | dict)

fusion_tools.visualization.vis_utils module

Utility functions for visualization components

fusion_tools.visualization.vis_utils.get_pattern_matching_value(input_val)

Used to extract usable values from components generated using pattern-matching syntax

Parameters:: input_val (None) – Value emitted by component generated with pattern-matching syntax
Returns:: Value used in callbacks
Return type:: None