Plot3d#

Plotting routines based on qt.

Note

This module is based on the pyqtgraph package.

Bases: object

One window in multi_plot.

imagesPath | str | np.ndarray | Source | List[Any] | List[List[Any]] (overlays): Typically, any that Plot3d already accepts

images: str | Path | ndarray | ClearMap.IO.source.Source | Sequence[str | Path | ndarray | ClearMap.IO.source.Source] | Sequence[Sequence[str | Path | ndarray | ClearMap.IO.source.Source]]#

lut: str | None = None#

max_projection: int | List[int] | None = None#

min_max: Tuple[float, float] | List[Tuple[float, float]] | None = None#

title: str | None = None#

arrange_plots(plots, screen=None, screen_percent=90)[source]#

bring_to_front(plots)[source]#

close(plots='all')[source]#

multi_plot(sources, axis=None, scale=None, title=None, invert_y=True, min_max=None, max_projection=None, arrange=True, screen=None, lut='flame', screen_percent=90, parent=None, sync=True, to_front=True)[source]#

Plot a source as 2d slices.

Arguments

sourceslist of sources: The sources to plot.If an element in the list is a list of sources those are overlayed in different colors in that window.
axisint or None: The axis along which to slice the data.
scaletuple of float: A spatial scale for each axis used for the spatial cursor position.
titlestr or None: The title of the window.
invert_ybool: If True invert the y axis (as typically done for images).
min_maxtuple or None: The minimal and maximal values for each source. If None, determine them from the source.
screenint or None: Specify on which screen to open the window.

Returns

plotslist of DataViewers: A list of viewer classes.

multi_plot_from_panels(panels: Sequence[PlotPanel], *, axis: int | None = None, scale: Tuple[float, float, float] | None = None, invert_y: bool = True, arrange: bool = True, sync: bool = True, screen: int | None = None, to_front: bool = True, parent=None)[source]#: Thin wrapper that converts a list of Panels into a call to multi_plot(). (same Path->str normalization as Plot3d.plot()).

plot(source, axis=None, scale=None, title=None, invert_y=True, min_max=None, screen=None, arrange=True, lut=None, max_projection=None, to_front=True, parent=None, sync=True)[source]#

Plot a source as 2d slices.

Arguments

sourceSource, pathlib.Path, list or dict: The source to plot. If a list is given several synchronized windows are generated. If an element in the list is a list of sources those are overlayed in different colors in that window.
axisint or None: The axis along which to slice the data.
scaletuple of float: A spatial scale for each axis used for the spatial cursor position.
titlestr or None: The title of the window.
invert_ybool: If True invert the y axis (as typically done for images).
min_maxtuple or None: The minimal and maximal values for each source. If None, determine them from the source.
screenint or None: Specify on which screen to open the window.

Returns

plotDataViewer: A data viewer class.

set_source(viewer, source)[source]#

Set the source data in a viewer.

Arguments

viewerDataViewer: The viewer to set a new source for.
sourceSource: The source to use in the viewer.

Returns

viewerDataViewer: The viewer.

synchronize(viewer1, viewer2)[source]#: Synchronize scrolling between two data viewers