Developers
Readers
- napari_deepfinder._reader.napari_get_reader(path)
A basic implementation of a Reader contribution.
Parameters
- pathstr or list of str
Path to file, or list of paths.
Returns
- function or None
If the path is a recognized format, return a function that accepts the same path or list of paths, and returns a list of layer data tuples.
- napari_deepfinder._reader.reader_function(path)
Take a path or list of paths and return a list of LayerData tuples.
Readers are expected to return data as a list of tuples, where each tuple is (data, [add_kwargs, [layer_type]]), “add_kwargs” and “layer_type” are both optional.
Parameters
- pathstr or list of str
Path to file, or list of paths.
Returns
- layer_datalist of tuples
A list of LayerData tuples where each tuple in the list contains (data, metadata, layer_type), where data is a numpy array, metadata is a dict of keyword arguments for the corresponding viewer.add_* method in napari, and layer_type is a lower-case string naming the type of layer. Both “meta”, and “layer_type” are optional. napari will default to layer_type==”image” if not provided
Writers
- napari_deepfinder._writer.write_annotations_xml(path: str, data: list)
Writer for annotations in for of a xml object list
- napari_deepfinder._writer.write_labelmap(path: str, data: array, meta: dict)
Writer for labelmaps (segmentation maps)
- napari_deepfinder._writer.write_tomogram(path: str, data: array, meta: dict)
Writer for tomograms
Widgets
Reorder layers
- napari_deepfinder._widget.reorder_widget()
Wrapper for a container of widgets representing a callable object.
Parameters
- functionCallable
A callable to turn into a GUI
- call_buttonbool | str | None, optional
If True, create an additional button that calls the original function when clicked. If a str, set the button text. by default False when auto_call is True, and True otherwise. The button can be accessed from the .call_button property.
- layoutstr, optional
The type of layout to use. Must be horizontal or vertical by default “horizontal”.
- scrollablebool, optional
Whether to enable scroll bars or not. If enabled, scroll bars will only appear along the layout direction, not in both directions.
- labelsbool, optional
Whether labels are shown in the widget. by default True
- tooltipsbool, optional
Whether tooltips are shown when hovering over widgets. by default True
- appApplication | str | None, optional
A backend to use, by default None (use the default backend.)
- visiblebool, optional
Whether to immediately show the widget. If False, widget is explicitly hidden. If None, widget is not shown, but will be shown if a parent container is shown, by default None.
- auto_callbool, optional
If True, changing any parameter in either the GUI or the widget attributes will call the original function with the current settings. by default False
- result_widgetbool, optional
Whether to display a LineEdit widget the output of the function when called, by default False
- param_optionsdict, optional
A dict of name: widget_options dict for each parameter in the function. Will be passed to magic_signature by default None
- namestr, optional
A name to assign to the Container widget, by default function.__name__
- persistbool, optional
If True, when parameter values change in the widget, they will be stored to disk (in ~/.config/magicgui/cache) and restored when the widget is loaded again with persist = True. By default, False.
- raise_on_unknownbool
If True, raise an error if a parameter annotation is not recognized.
Raises
- TypeError
If unexpected keyword arguments are provided
Denoising
- napari_deepfinder._widget.denoise_widget()
Wrapper for a container of widgets representing a callable object.
Parameters
- functionCallable
A callable to turn into a GUI
- call_buttonbool | str | None, optional
If True, create an additional button that calls the original function when clicked. If a str, set the button text. by default False when auto_call is True, and True otherwise. The button can be accessed from the .call_button property.
- layoutstr, optional
The type of layout to use. Must be horizontal or vertical by default “horizontal”.
- scrollablebool, optional
Whether to enable scroll bars or not. If enabled, scroll bars will only appear along the layout direction, not in both directions.
- labelsbool, optional
Whether labels are shown in the widget. by default True
- tooltipsbool, optional
Whether tooltips are shown when hovering over widgets. by default True
- appApplication | str | None, optional
A backend to use, by default None (use the default backend.)
- visiblebool, optional
Whether to immediately show the widget. If False, widget is explicitly hidden. If None, widget is not shown, but will be shown if a parent container is shown, by default None.
- auto_callbool, optional
If True, changing any parameter in either the GUI or the widget attributes will call the original function with the current settings. by default False
- result_widgetbool, optional
Whether to display a LineEdit widget the output of the function when called, by default False
- param_optionsdict, optional
A dict of name: widget_options dict for each parameter in the function. Will be passed to magic_signature by default None
- namestr, optional
A name to assign to the Container widget, by default function.__name__
- persistbool, optional
If True, when parameter values change in the widget, they will be stored to disk (in ~/.config/magicgui/cache) and restored when the widget is loaded again with persist = True. By default, False.
- raise_on_unknownbool
If True, raise an error if a parameter annotation is not recognized.
Raises
- TypeError
If unexpected keyword arguments are provided
Annotation
- class napari_deepfinder._widget.AddPointsWidget(napari_viewer: Viewer)
Widget to add points to layer. This is especially designed for tomogram annotation in Orthoslice view.