biotite.AdaptiveFancyArrow¶

class biotite.AdaptiveFancyArrow(x, y, dx, dy, tail_width, head_width, head_ratio, draw_head=True, shape='full', **kwargs)[source]¶

Bases: FancyArrow

A FancyArrow with fixed head shape.

The length of the head is proportional to the width of the head in display coordinates. If the head length is longer than the length of the entire arrow, the head length is limited to the arrow length.

Parameters

x,yfloat: The arrow’s start position.
dx, dyfloat: The arrow’s direction vector, inclduing the arrow head.
tail_width, head_widthfloat: The width of the arrow’s tail and head in its reference coordinate system
head_ratiofloat, optional: The length of the arrow head as faction of the arrow width (display coordinates).
draw_head: bool, optional: If false, the arrow has no head. The result is a rectangle.
shapestr, optional: The shape parameter in the constructor of FancyArrow.
**kwargs: Other parameters that are used in the constructor of FancyArrow.

add_callback(func)¶

Add a callback function that will be called whenever one of the .Artist’s properties changes.

Parameters

funccallable

The callback function. It must have the signature:

def func(artist: Artist) -> Any

where artist is the calling .Artist. Return values may exist but are ignored.

Returns

int: The observer id associated with the callback. This id can be used for removing the callback with .remove_callback later.

See also

remove_callback

contains(mouseevent, radius=None)¶

Test whether the mouse event occurred in the patch.

Returns

(bool, empty dict)

contains_point(point, radius=None)¶

Return whether the given point is inside the patch.

Parameters

point(float, float): The point (x, y) to check, in target coordinates of self.get_transform(). These are display coordinates for patches that are added to a figure or axes.
radiusfloat, optional: Additional margin on the patch in target coordinates of self.get_transform(). See .Path.contains_point for further details.

Returns

bool

Notes

The proper use of this method depends on the transform of the patch. Isolated patches do not have a transform. In this case, the patch creation coordinates and the point coordinates match. The following example checks that the center of a circle is within the circle

>>> center = 0, 0
>>> c = Circle(center, radius=1)
>>> c.contains_point(center)
True

The convention of checking against the transformed patch stems from the fact that this method is predominantly used to check if display coordinates (e.g. from mouse events) are within the patch. If you want to do the above check with data coordinates, you have to properly transform them first:

>>> center = 0, 0
>>> c = Circle(center, radius=1)
>>> plt.gca().add_patch(c)
>>> transformed_center = c.get_transform().transform(center)
>>> c.contains_point(transformed_center)
True

contains_points(points, radius=None)¶

Return whether the given points are inside the patch.

Parameters

points(N, 2) array: The points to check, in target coordinates of self.get_transform(). These are display coordinates for patches that are added to a figure or axes. Columns contain x and y values.
radiusfloat, optional: Additional margin on the patch in target coordinates of self.get_transform(). See .Path.contains_point for further details.

Returns

length-N bool array

Notes

The proper use of this method depends on the transform of the patch. See the notes on .Patch.contains_point.

convert_xunits(x)¶

Convert x using the unit type of the xaxis.

If the artist is not contained in an Axes or if the xaxis does not have units, x itself is returned.

convert_yunits(y)¶

Convert y using the unit type of the yaxis.

If the artist is not contained in an Axes or if the yaxis does not have units, y itself is returned.

draw(renderer)¶

Draw the Artist (and its children) using the given renderer.

This has no effect if the artist is not visible (.Artist.get_visible returns False).

Parameters

renderer~matplotlib.backend_bases.RendererBase subclass.

Notes

This method is overridden in the Artist subclasses.

findobj(match=None, include_self=True)¶

Find artist objects.

Recursively find all .Artist instances contained in the artist.

Parameters

match

A filter criterion for the matches. This can be

None: Return all objects contained in artist.
A function with signature def match(artist: Artist) -> bool. The result will only contain artists for which the function returns True.
A class instance: e.g., .Line2D. The result will only contain artists of this class or its subclasses (isinstance check).

include_selfbool

Include self in the list to be checked for a match.

Returns

list of .Artist

format_cursor_data(data)¶

Return a string representation of data.

Note

This method is intended to be overridden by artist subclasses. As an end-user of Matplotlib you will most likely not call this method yourself.

The default implementation converts ints and floats and arrays of ints and floats into a comma-separated string enclosed in square brackets, unless the artist has an associated colorbar, in which case scalar values are formatted using the colorbar’s formatter.

See also

get_cursor_data

get_aa()¶: Alias for get_antialiased.

get_agg_filter()¶: Return filter function to be used for agg filter.

get_alpha()¶: Return the alpha value used for blending - not supported on all backends.

get_animated()¶: Return whether the artist is animated.

get_antialiased()¶: Return whether antialiasing is used for drawing.

get_capstyle()¶: Return the capstyle.

get_children()¶: Return a list of the child .Artists of this .Artist.

get_clip_box()¶: Return the clipbox.

get_clip_on()¶: Return whether the artist uses clipping.

get_clip_path()¶: Return the clip path.

get_closed()¶: Return whether the polygon is closed.

get_cursor_data(event)¶

Return the cursor data for a given event.

Note

This method is intended to be overridden by artist subclasses. As an end-user of Matplotlib you will most likely not call this method yourself.

Cursor data can be used by Artists to provide additional context information for a given event. The default implementation just returns None.

Subclasses can override the method and return arbitrary data. However, when doing so, they must ensure that .format_cursor_data can convert the data to a string representation.

The only current use case is displaying the z-value of an .AxesImage in the status bar of a plot window, while moving the mouse.

Parameters

event~matplotlib.backend_bases.MouseEvent

See also

format_cursor_data

get_data_transform()¶: Return the ~.transforms.Transform mapping data coordinates to physical coordinates.

get_ec()¶: Alias for get_edgecolor.

get_edgecolor()¶: Return the edge color.

get_extents()¶: Return the Patch’s axis-aligned extents as a ~.transforms.Bbox.

get_facecolor()¶: Return the face color.

get_fc()¶: Alias for get_facecolor.

get_figure()¶: Return the .Figure instance the artist belongs to.

get_fill()¶: Return whether the patch is filled.

get_gid()¶: Return the group id.

get_hatch()¶: Return the hatching pattern.

get_in_layout()¶

get_joinstyle()¶: Return the joinstyle.

get_label()¶: Return the label used for this artist in the legend.

get_linestyle()¶: Return the linestyle.

get_linewidth()¶: Return the line width in points.

get_ls()¶: Alias for get_linestyle.

get_lw()¶: Alias for get_linewidth.

get_mouseover()¶: Return whether this artist is queried for custom context information when the mouse cursor moves over it.

get_patch_transform()¶

Return the ~.transforms.Transform instance mapping patch coordinates to data coordinates.

For example, one may define a patch of a circle which represents a radius of 5 by providing coordinates for a unit circle, and a transform which scales the coordinates (the patch coordinate) by 5.

get_path()¶: Get the .Path of the polygon.

get_path_effects()¶

get_picker()¶

Return the picking behavior of the artist.

The possible values are described in .set_picker.

See also

set_picker, pickable, pick

get_rasterized()¶: Return whether the artist is to be rasterized.

get_sketch_params()¶

Return the sketch parameters for the artist.

Returns

tuple or None

A 3-tuple with the following elements:

scale: The amplitude of the wiggle perpendicular to the source line.
length: The length of the wiggle along the line.
randomness: The scale factor by which the length is shrunken or expanded.

Returns None if no sketch parameters were set.

get_snap()¶

Return the snap setting.

See .set_snap for details.

get_tightbbox(renderer=None)¶

Like .Artist.get_window_extent, but includes any clipping.

Parameters

renderer~matplotlib.backend_bases.RendererBase subclass, optional: renderer that will be used to draw the figures (i.e. fig.canvas.get_renderer())

Returns

.Bbox or None: The enclosing bounding box (in figure pixel coordinates). Returns None if clipping results in no intersection.

get_transform()¶: Return the ~.transforms.Transform applied to the Patch.

get_transformed_clip_path_and_affine()¶: Return the clip path with the non-affine part of its transformation applied, and the remaining affine part of its transformation.

get_url()¶: Return the url.

get_verts()¶

Return a copy of the vertices used in this patch.

If the patch contains Bézier curves, the curves will be interpolated by line segments. To access the curves as curves, use get_path.

get_visible()¶: Return the visibility.

get_window_extent(renderer=None)¶

Get the artist’s bounding box in display space.

The bounding box’ width and height are nonnegative.

Subclasses should override for inclusion in the bounding box “tight” calculation. Default is to return an empty bounding box at 0, 0.

Be careful when using this function, the results will not update if the artist window extent of the artist changes. The extent can change due to any changes in the transform stack, such as changing the axes limits, the figure size, or the canvas used (as is done when saving a figure). This can lead to unexpected behavior where interactive figures will look fine on the screen, but will save incorrectly.

get_xy()¶

Get the vertices of the path.

Returns

(N, 2) array: The coordinates of the vertices.

get_zorder()¶: Return the artist’s zorder.

have_units()¶: Return whether units are set on any axis.

is_transform_set()¶

Return whether the Artist has an explicitly set transform.

This is True after .set_transform has been called.

pchanged()¶

Call all of the registered callbacks.

This function is triggered internally when a property is changed.

See also

add_callback
remove_callback

pick(mouseevent)¶

Process a pick event.

Each child artist will fire a pick event if mouseevent is over the artist and the artist has picker set.

See also

set_picker, get_picker, pickable

pickable()¶

Return whether the artist is pickable.

See also

set_picker, get_picker, pick

properties()¶: Return a dictionary of all the properties of the artist.

remove()¶

Remove the artist from the figure if possible.

The effect will not be visible until the figure is redrawn, e.g., with .FigureCanvasBase.draw_idle. Call ~.axes.Axes.relim to update the axes limits if desired.

Note: ~.axes.Axes.relim will not see collections even if the collection was added to the axes with autolim = True.

Note: there is no support for removing the artist’s legend entry.

remove_callback(oid)¶

Remove a callback based on its observer id.

See also

add_callback

set(*, agg_filter=<UNSET>, alpha=<UNSET>, animated=<UNSET>, antialiased=<UNSET>, capstyle=<UNSET>, clip_box=<UNSET>, clip_on=<UNSET>, clip_path=<UNSET>, closed=<UNSET>, color=<UNSET>, data=<UNSET>, edgecolor=<UNSET>, facecolor=<UNSET>, fill=<UNSET>, gid=<UNSET>, hatch=<UNSET>, in_layout=<UNSET>, joinstyle=<UNSET>, label=<UNSET>, linestyle=<UNSET>, linewidth=<UNSET>, mouseover=<UNSET>, path_effects=<UNSET>, picker=<UNSET>, rasterized=<UNSET>, sketch_params=<UNSET>, snap=<UNSET>, transform=<UNSET>, url=<UNSET>, visible=<UNSET>, xy=<UNSET>, zorder=<UNSET>)¶

Set multiple properties at once.

Supported properties are

Properties:: agg_filter: a filter function, which takes a (m, n, 3) float array and a dpi value, and returns a (m, n, 3) array and two offsets from the bottom left corner of the image alpha: scalar or None animated: bool antialiased or aa: bool or None capstyle: .CapStyle or {‘butt’, ‘projecting’, ‘round’} clip_box: ~matplotlib.transforms.BboxBase or None clip_on: bool clip_path: Patch or (Path, Transform) or None closed: bool color: color data: unknown edgecolor or ec: color or None facecolor or fc: color or None figure: ~matplotlib.figure.Figure fill: bool gid: str hatch: {‘/’, ‘\’, ‘|’, ‘-‘, ‘+’, ‘x’, ‘o’, ‘O’, ‘.’, ‘*’} in_layout: unknown joinstyle: .JoinStyle or {‘miter’, ‘round’, ‘bevel’} label: object linestyle or ls: {‘-‘, ‘–’, ‘-.’, ‘:’, ‘’, (offset, on-off-seq), …} linewidth or lw: float or None mouseover: bool path_effects: list of .AbstractPathEffect picker: None or bool or float or callable rasterized: bool sketch_params: (scale: float, length: float, randomness: float) snap: bool or None transform: ~matplotlib.transforms.Transform url: str visible: bool xy: (N, 2) array-like zorder: float

set_aa(aa)¶: Alias for set_antialiased.

set_agg_filter(filter_func)¶

Set the agg filter.

Parameters

filter_funccallable: A filter function, which takes a (m, n, depth) float array and a dpi value, and returns a (m, n, depth) array and two offsets from the bottom left corner of the image

set_alpha(alpha)¶

Set the alpha value used for blending - not supported on all backends.

Parameters

alphascalar or None: alpha must be within the 0-1 range, inclusive.

set_animated(b)¶

Set whether the artist is intended to be used in an animation.

If True, the artist is excluded from regular drawing of the figure. You have to call .Figure.draw_artist / .Axes.draw_artist explicitly on the artist. This approach is used to speed up animations using blitting.

See also matplotlib.animation and blitting.

Parameters

bbool

set_antialiased(aa)¶

Set whether to use antialiased rendering.

Parameters

aabool or None

set_capstyle(s)¶

Set the .CapStyle.

The default capstyle is ‘round’ for .FancyArrowPatch and ‘butt’ for all other patches.

Parameters

s.CapStyle or {‘butt’, ‘projecting’, ‘round’}

set_clip_box(clipbox)¶

Set the artist’s clip .Bbox.

Parameters

clipbox~matplotlib.transforms.BboxBase or None: Will typically be created from a .TransformedBbox. For instance, TransformedBbox(Bbox([[0, 0], [1, 1]]), ax.transAxes) is the default clipping for an artist added to an Axes.

set_clip_on(b)¶

Set whether the artist uses clipping.

When False, artists will be visible outside the Axes which can lead to unexpected results.

Parameters

bbool

set_clip_path(path, transform=None)¶

Set the artist’s clip path.

Parameters

path~matplotlib.patches.Patch or .Path or .TransformedPath or None: The clip path. If given a .Path, transform must be provided as well. If None, a previously set clip path is removed.
transform~matplotlib.transforms.Transform, optional: Only used if path is a .Path, in which case the given .Path is converted to a .TransformedPath using transform.

Notes

For efficiency, if path is a .Rectangle this method will set the clipping box to the corresponding rectangle and set the clipping path to None.

For technical reasons (support of ~.Artist.set), a tuple (path, transform) is also accepted as a single positional parameter.

set_closed(closed)¶

Set whether the polygon is closed.

Parameters

closedbool: True if the polygon is closed

set_color(c)¶

Set both the edgecolor and the facecolor.

Parameters

ccolor

See also

Patch.set_facecolor, Patch.set_edgecolor: For setting the edge or face color individually.

set_data(*, x=None, y=None, dx=None, dy=None, width=None, head_width=None, head_length=None)¶

Set .FancyArrow x, y, dx, dy, width, head_with, and head_length. Values left as None will not be updated.

Parameters

x, yfloat or None, default: None: The x and y coordinates of the arrow base.
dx, dyfloat or None, default: None: The length of the arrow along x and y direction.
widthfloat or None, default: None: Width of full arrow tail.
head_widthfloat or None, default: None: Total width of the full arrow head.
head_lengthfloat or None, default: None: Length of arrow head.

set_ec(color)¶: Alias for set_edgecolor.

set_edgecolor(color)¶

Set the patch edge color.

Parameters

colorcolor or None

set_facecolor(color)¶

Set the patch face color.

Parameters

colorcolor or None

set_fc(color)¶: Alias for set_facecolor.

set_figure(fig)¶

Set the .Figure instance the artist belongs to.

Parameters

fig~matplotlib.figure.Figure

set_fill(b)¶

Set whether to fill the patch.

Parameters

bbool

set_gid(gid)¶

Set the (group) id for the artist.

Parameters

gidstr

set_hatch(hatch)¶

Set the hatching pattern.

hatch can be one of:

/   - diagonal hatching
\   - back diagonal
|   - vertical
-   - horizontal
+   - crossed
x   - crossed diagonal
o   - small circle
O   - large circle
.   - dots
*   - stars

Letters can be combined, in which case all the specified hatchings are done. If same letter repeats, it increases the density of hatching of that pattern.

Hatching is supported in the PostScript, PDF, SVG and Agg backends only.

Parameters

hatch{‘/’, ‘\’, ‘|’, ‘-‘, ‘+’, ‘x’, ‘o’, ‘O’, ‘.’, ‘*’}

set_in_layout(in_layout)¶

set_joinstyle(s)¶

Set the .JoinStyle.

The default joinstyle is ‘round’ for .FancyArrowPatch and ‘miter’ for all other patches.

Parameters

s.JoinStyle or {‘miter’, ‘round’, ‘bevel’}

set_label(s)¶

Set a label that will be displayed in the legend.

Parameters

sobject: s will be converted to a string by calling str.

set_linestyle(ls)¶

Set the patch linestyle.

linestyle	description
`'-'` or `'solid'`	solid line
`'--'` or `'dashed'`	dashed line
`'-.'` or `'dashdot'`	dash-dotted line
`':'` or `'dotted'`	dotted line
`'none'`, `'None'`, `' '`, or `''`	draw nothing

Alternatively a dash tuple of the following form can be provided:

(offset, onoffseq)

where onoffseq is an even length tuple of on and off ink in points.

Parameters

ls{‘-‘, ‘–’, ‘-.’, ‘:’, ‘’, (offset, on-off-seq), …}: The line style.

set_linewidth(w)¶

Set the patch linewidth in points.

Parameters

wfloat or None

set_ls(ls)¶: Alias for set_linestyle.

set_lw(w)¶: Alias for set_linewidth.

set_mouseover(mouseover)¶

Set whether this artist is queried for custom context information when the mouse cursor moves over it.

Parameters

mouseoverbool

See also

get_cursor_data
ToolCursorPosition
NavigationToolbar2

set_path_effects(path_effects)¶

Set the path effects.

Parameters

path_effectslist of .AbstractPathEffect

set_picker(picker)¶

Define the picking behavior of the artist.

Parameters

pickerNone or bool or float or callable

This can be one of the following:

None: Picking is disabled for this artist (default).
A boolean: If True then picking will be enabled and the artist will fire a pick event if the mouse event is over the artist.
A float: If picker is a number it is interpreted as an epsilon tolerance in points and the artist will fire off an event if its data is within epsilon of the mouse event. For some artists like lines and patch collections, the artist may provide additional data to the pick event that is generated, e.g., the indices of the data within epsilon of the pick event
A function: If picker is callable, it is a user supplied function which determines whether the artist is hit by the mouse event:
```
hit, props = picker(artist, mouseevent)
```
to determine the hit test. if the mouse event is over the artist, return hit=True and props is a dictionary of properties you want added to the PickEvent attributes.

set_rasterized(rasterized)¶

Force rasterized (bitmap) drawing for vector graphics output.

Rasterized drawing is not supported by all artists. If you try to enable this on an artist that does not support it, the command has no effect and a warning will be issued.

This setting is ignored for pixel-based output.

See also /gallery/misc/rasterization_demo.

Parameters

rasterizedbool

set_sketch_params(scale=None, length=None, randomness=None)¶

Set the sketch parameters.

Parameters

scalefloat, optional

The amplitude of the wiggle perpendicular to the source line, in pixels. If scale is None, or not provided, no sketch filter will be provided.

lengthfloat, optional

The length of the wiggle along the line, in pixels (default 128.0)

randomnessfloat, optional

The scale factor by which the length is shrunken or expanded (default 16.0)

The PGF backend uses this argument as an RNG seed and not as described above. Using the same seed yields the same random shape.

set_snap(snap)¶

Set the snapping behavior.

Snapping aligns positions with the pixel grid, which results in clearer images. For example, if a black line of 1px width was defined at a position in between two pixels, the resulting image would contain the interpolated value of that line in the pixel grid, which would be a grey value on both adjacent pixel positions. In contrast, snapping will move the line to the nearest integer pixel value, so that the resulting image will really contain a 1px wide black line.

Snapping is currently only supported by the Agg and MacOSX backends.

Parameters

snapbool or None

Possible values:

True: Snap vertices to the nearest pixel center.
False: Do not modify vertex positions.
None: (auto) If the path contains only rectilinear line segments, round to the nearest pixel center.

set_transform(t)¶

Set the artist transform.

Parameters

t~matplotlib.transforms.Transform

set_url(url)¶

Set the url for the artist.

Parameters

urlstr

set_visible(b)¶

Set the artist’s visibility.

Parameters

bbool

set_xy(xy)¶

Set the vertices of the polygon.

Parameters

xy(N, 2) array-like: The coordinates of the vertices.

Notes

Unlike .Path, we do not ignore the last input vertex. If the polygon is meant to be closed, and the last point of the polygon is not equal to the first, we assume that the user has not explicitly passed a CLOSEPOLY vertex, and add it ourselves.

set_zorder(level)¶

Set the zorder for the artist. Artists with lower zorder values are drawn first.

Parameters