import typing
from pathlib import Path
from typing import Optional, Union
from weakref import WeakSet
import magicgui as mgui
import numpy as np
from napari.components.viewer_model import ViewerModel
from napari.utils import _magicgui
from napari.utils.events.event_utils import disconnect_events
if typing.TYPE_CHECKING:
# helpful for IDE support
from napari._qt.qt_main_window import Window
[docs]
@mgui.register_type(bind=_magicgui.proxy_viewer_ancestor)
class Viewer(ViewerModel):
"""Napari ndarray viewer.
Parameters
----------
title : string, optional
The title of the viewer window. By default 'napari'.
ndisplay : {2, 3}, optional
Number of displayed dimensions. By default 2.
order : tuple of int, optional
Order in which dimensions are displayed where the last two or last
three dimensions correspond to row x column or plane x row x column if
ndisplay is 2 or 3. By default None
axis_labels : list of str, optional
Dimension names. By default they are labeled with sequential numbers
show : bool, optional
Whether to show the viewer after instantiation. By default True.
"""
_window: 'Window' = None # type: ignore
_instances: typing.ClassVar[WeakSet['Viewer']] = WeakSet()
def __init__(
self,
*,
title='napari',
ndisplay=2,
order=(),
axis_labels=(),
show=True,
**kwargs,
) -> None:
super().__init__(
title=title,
ndisplay=ndisplay,
order=order,
axis_labels=axis_labels,
**kwargs,
)
# we delay initialization of plugin system to the first instantiation
# of a viewer... rather than just on import of plugins module
from napari.plugins import _initialize_plugins
# having this import here makes all of Qt imported lazily, upon
# instantiating the first Viewer.
from napari.window import Window
_initialize_plugins()
self._window = Window(self, show=show)
self._instances.add(self)
# Expose private window publicly. This is needed to keep window off pydantic model
@property
def window(self) -> 'Window':
return self._window
[docs]
def update_console(self, variables):
"""Update console's namespace with desired variables.
Parameters
----------
variables : dict, str or list/tuple of str
The variables to inject into the console's namespace. If a dict, a
simple update is done. If a str, the string is assumed to have
variable names separated by spaces. A list/tuple of str can also
be used to give the variable names. If just the variable names are
give (list/tuple/str) then the variable values looked up in the
callers frame.
"""
if self.window._qt_viewer._console is None:
self.window._qt_viewer.add_to_console_backlog(variables)
return
self.window._qt_viewer.console.push(variables)
[docs]
def export_rois(
self,
rois: list[np.ndarray],
paths: Optional[Union[str, Path, list[Union[str, Path]]]] = None,
scale: Optional[float] = None,
):
"""Export the given rectangular rois to specified file paths.
Iteratively take a screenshot of each given roi. Note that 3D rois
or taking rois when number of dimensions displayed in the viewer
canvas is 3, is currently not supported.
Parameters
----------
rois: numpy array
A list of arrays with each having shape (4, 2) representing a
rectangular roi.
paths: str, Path, list[str, Path], optional
Where to save the rois. If a string or a Path, a directory will
be created if it does not exist yet and screenshots will be saved
with filename `roi_{n}.png` where n is the nth roi. If paths is
a list of either string or paths, these need to be the full paths
of where to store each individual roi. In this case
the length of the list and the number of rois must match.
If None, the screenshots will only be returned
and not saved to disk.
scale: float, optional
Scale factor used to increase resolution of canvas for the screenshot.
By default, uses the displayed scale.
Returns
-------
screenshot_list: list
The list containing all the screenshots.
"""
# Check to see if roi has shape (n,2,2)
if any(roi.shape[-2:] != (4, 2) for roi in rois):
raise ValueError(
'ROI found with invalid shape, all rois must have shape (4, 2), i.e. have 4 corners defined in 2 '
'dimensions. 3D is not supported.'
)
screenshot_list = self.window.export_rois(
rois, paths=paths, scale=scale
)
return screenshot_list
[docs]
def screenshot(
self,
path: Optional[str] = None,
*,
size: Optional[tuple[str, str]] = None,
scale: Optional[float] = None,
canvas_only: bool = True,
flash: bool = False,
):
"""Take currently displayed screen and convert to an image array.
Parameters
----------
path : str, optional
Filename for saving screenshot image.
size : tuple of two ints, optional
Size (resolution height x width) of the screenshot. By default, the currently
displayed size. Only used if `canvas_only` is True.
scale : float, optional
Scale factor used to increase resolution of canvas for the screenshot.
By default, the currently displayed resolution.Only used if `canvas_only` is
True.
canvas_only : bool
If True, screenshot shows only the image display canvas, and if False include
the napari viewer frame in the screenshot, By default, True.
flash : bool
Flag to indicate whether flash animation should be shown after
the screenshot was captured.
By default, False.
Returns
-------
image : array
Numpy array of type ubyte and shape (h, w, 4). Index [0, 0] is the
upper-left corner of the rendered region.
"""
return self.window.screenshot(
path=path,
size=size,
scale=scale,
flash=flash,
canvas_only=canvas_only,
)
[docs]
def show(self, *, block=False):
"""Resize, show, and raise the viewer window."""
self.window.show(block=block)
[docs]
def close(self):
"""Close the viewer window."""
# Shutdown the slicer first to avoid processing any more tasks.
self._layer_slicer.shutdown()
# Disconnect changes to dims before removing layers one-by-one
# to avoid any unnecessary slicing.
disconnect_events(self.dims.events, self)
# Remove all the layers from the viewer
self.layers.clear()
# Close the main window
self.window.close()
self._instances.discard(self)
[docs]
@classmethod
def close_all(cls) -> int:
"""
Class method, Close all existing viewer instances.
This is mostly exposed to avoid leaking of viewers when running tests.
As having many non-closed viewer can adversely affect performances.
It will return the number of viewer closed.
Returns
-------
int
number of viewer closed.
"""
# copy to not iterate while changing.
viewers = list(cls._instances)
ret = len(viewers)
for viewer in viewers:
viewer.close()
return ret
[docs]
def current_viewer() -> Optional[Viewer]:
"""Return the currently active napari viewer."""
try:
from napari._qt.qt_main_window import _QtMainWindow
except ImportError:
return None
else:
return _QtMainWindow.current_viewer()
