Module `bioiain.visualisation.plots`

Functions

def fig2D(**kwargs)

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def fig2D(**kwargs):
    fig = plt.figure(**kwargs)
    ax = fig.add_subplot(111)
    ax.set_aspect('equal')
    return fig, ax

def fig3D(entity: = None, preset: str = None, fig: matplotlib.figure.Figure = None, ax: matplotlib.axes._axes.Axes = None) ‑> list[matplotlib.figure.Figure | matplotlib.axes._axes.Axes]

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def fig3D(entity:any=None, preset:str=None,
          fig:mpl.pyplot.Figure=None,
          ax:mpl.pyplot.Axes=None) -> list[mpl.pyplot.Figure|mpl.pyplot.Axes]:
    """
    Initialises a 3-Dimensional Matplotlib plot, optionally using a preset.
    :param entity: (Optional) The entity to plot, might be required in some presets.
    :param preset: Name of preset to use.
    :param fig: Use this figure instead of new one.
    :param ax: Use these axes instead of new ones.
    :return: Figures and Axes generated.
    """
    if fig is None:
        fig = plt.figure()
    if ax is None:
        ax = fig.add_subplot(111, projection='3d')
    ax.set_aspect('equal')

    if preset == "crystal-frac":
        ax.set_xticks([-1, 0, 1, 2])
        ax.set_yticks([-1, 0, 1, 2])
        ax.set_zticks([-1, 0, 1, 2])

        ax.set_xlabel("X")
        ax.set_ylabel("Y")
        ax.set_zlabel("Z")

        ax.axes.set_xlim(-1,2)
        ax.axes.set_ylim(-1,2)
        ax.axes.set_zlim(-1,2)

    else:
        log("warning", "3D Plot preset ({}) not found".format(preset))


    return [fig, ax]

Initialises a 3-Dimensional Matplotlib plot, optionally using a preset. :param entity: (Optional) The entity to plot, might be required in some presets. :param preset: Name of preset to use. :param fig: Use this figure instead of new one. :param ax: Use these axes instead of new ones. :return: Figures and Axes generated.

def grid2D(rows, columns, height=5, width=5, as_grid=False)

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def grid2D(rows, columns, height=5, width=5, as_grid=False):
    log(2, f"Creating {rows}x{columns} (rxc) grid...")
    fig, grid_axes = plt.subplots(rows, columns, figsize=(columns*width, rows*height))
    if as_grid:
        return fig, grid_axes
    axes = []
    for row in grid_axes:
        axes.extend(row)

    return fig, axes

def plot_confusion(preds, labels, title, score=None, classes=None)

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def plot_confusion(preds, labels, title, score=None, classes=None):
    try:
        log(1, "Plotting confusion...")
        cm = confusion_matrix(labels, preds)
        if classes is None:
            classes = list(set(labels))
        plt.figure(figsize=(1*len(classes) ,1*len(classes)))
        sb.heatmap(cm, annot=True, fmt="d", cmap="Blues", xticklabels=classes, yticklabels=classes)
        plt.xlabel("Predicted")
        plt.ylabel("True")
        if score is not None:
            title = f"{title}_S={score:.2f}"
        plt.title(title)
        os.makedirs("figs", exist_ok=True)
        path = f"figs/{title}.confusion.png"
        plt.savefig(path)
        plt.close()
        return cm, path
    except Exception as e:
        print(e)

def plot_heatmap(matrix, show=False, filename=None)

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def plot_heatmap(matrix, show=False, filename=None):
    fig = plt.figure()
    ax = fig.add_subplot()

    ax.imshow(matrix)
    if filename is not None:
        plt.savefig(filename)
    if show:
        plt.show(block=True)

Classes

class Arrow3D (xs, ys, zs, *args, **kwargs)

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class Arrow3D(FancyArrowPatch):
    def __init__(self, xs, ys, zs, *args, **kwargs):
        arrow_prop_dict = dict(mutation_scale=20, arrowstyle='-|>', color='k', shrinkA=0, shrinkB=0)
        kwargs = arrow_prop_dict | kwargs
        super().__init__((0,0), (0,0), *args, **kwargs)
        self._verts3d = xs, ys, zs

    def do_3d_projection(self, renderer=None):
        xs3d, ys3d, zs3d = self._verts3d
        xs, ys, zs = proj3d.proj_transform(xs3d, ys3d, zs3d, self.axes.M)
        self.set_positions((xs[0],ys[0]),(xs[1],ys[1]))

        return np.min(zs)

A fancy arrow patch.

It draws an arrow using the ArrowStyle. It is primarily used by the ~.axes.Axes.annotate method. For most purposes, use the annotate method for drawing arrows.

The head and tail positions are fixed at the specified start and end points of the arrow, but the size and shape (in display coordinates) of the arrow does not change when the axis is moved or zoomed.

Defining the arrow position and path

There are two ways to define the arrow position and path:

Start, end and connection: The typical approach is to define the start and end points of the arrow using posA and posB. The curve between these two can further be configured using connectionstyle.

If given, the arrow curve is clipped by patchA and patchB, allowing it to start/end at the border of these patches. Additionally, the arrow curve can be shortened by shrinkA and shrinkB to create a margin between start/end (after possible clipping) and the drawn arrow.

path: Alternatively if path is provided, an arrow is drawn along this Path. In this case, connectionstyle, patchA, patchB, shrinkA, and shrinkB are ignored.

Styling

The arrowstyle defines the styling of the arrow head, tail and shaft. The resulting arrows can be styled further by setting the .Patch properties such as linewidth, color, facecolor, edgecolor etc. via keyword arguments.

Parameters

posA, posB : (float, float), optional

(x, y) coordinates of start and end point of the arrow. The actually drawn start and end positions may be modified through patchA, patchB, shrinkA, and shrinkB.

posA, posB are exclusive of path.

path : ~matplotlib.path.Path, optional

If provided, an arrow is drawn along this path and patchA, patchB, shrinkA, and shrinkB are ignored.

path is exclusive of posA, posB.

arrowstyle : str or .ArrowStyle, default: 'simple'

The styling of arrow head, tail and shaft. This can be

.ArrowStyle or one of its subclasses
The shorthand string name (e.g. "->") as given in the table below, optionally containing a comma-separated list of style parameters, e.g. "->, head_length=10, head_width=5".

The style parameters are scaled by mutation_scale.

The following arrow styles are available. See also :doc:/gallery/text_labels_and_annotations/fancyarrow_demo.

============= ========== =============================================================================================================================== Class Name Parameters
============= ========== =============================================================================================================================== Curve - None
CurveA <- head_length=0.4, head_width=0.2, widthA=1.0, widthB=1.0, lengthA=0.2, lengthB=0.2, angleA=0, angleB=0, scaleA=None, scaleB=None CurveB -> head_length=0.4, head_width=0.2, widthA=1.0, widthB=1.0, lengthA=0.2, lengthB=0.2, angleA=0, angleB=0, scaleA=None, scaleB=None CurveAB <-> head_length=0.4, head_width=0.2, widthA=1.0, widthB=1.0, lengthA=0.2, lengthB=0.2, angleA=0, angleB=0, scaleA=None, scaleB=None CurveFilledA <|- head_length=0.4, head_width=0.2, widthA=1.0, widthB=1.0, lengthA=0.2, lengthB=0.2, angleA=0, angleB=0, scaleA=None, scaleB=None CurveFilledB -|> head_length=0.4, head_width=0.2, widthA=1.0, widthB=1.0, lengthA=0.2, lengthB=0.2, angleA=0, angleB=0, scaleA=None, scaleB=None CurveFilledAB <|-|> head_length=0.4, head_width=0.2, widthA=1.0, widthB=1.0, lengthA=0.2, lengthB=0.2, angleA=0, angleB=0, scaleA=None, scaleB=None BracketA ]- widthA=1.0, lengthA=0.2, angleA=0
BracketB -[ widthB=1.0, lengthB=0.2, angleB=0
BracketAB ]-[ widthA=1.0, lengthA=0.2, angleA=0, widthB=1.0, lengthB=0.2, angleB=0
BarAB |-| widthA=1.0, angleA=0, widthB=1.0, angleB=0
BracketCurve ]-> widthA=1.0, lengthA=0.2, angleA=None
CurveBracket <-[ widthB=1.0, lengthB=0.2, angleB=None
Simple simple head_length=0.5, head_width=0.5, tail_width=0.2
Fancy fancy head_length=0.4, head_width=0.4, tail_width=0.4
Wedge wedge tail_width=0.3, shrink_factor=0.5
============= ========== ===============================================================================================================================

Only the styles <|-, -|>, <|-|> simple, fancy and wedge contain closed paths and can be filled.

connectionstyle : str or .ConnectionStyle or None, optional, default: 'arc3'

.ConnectionStyle with which posA and posB are connected. This can be

.ConnectionStyle or one of its subclasses
The shorthand string name as given in the table below, e.g. "arc3".

====== ========== ================================================= Class Name Parameters
====== ========== ================================================= Arc3 arc3 rad=0.0
Angle3 angle3 angleA=90, angleB=0
Angle angle angleA=90, angleB=0, rad=0.0
Arc arc angleA=0, angleB=0, armA=None, armB=None, rad=0.0 Bar bar armA=0.0, armB=0.0, fraction=0.3, angle=None
====== ========== =================================================

Ignored if path is provided.

patchA, patchB : ~matplotlib.patches.Patch, default: None

Optional Patches at posA and posB, respectively. If given, the arrow path is clipped by these patches such that head and tail are at the border of the patches.

Ignored if path is provided.

shrinkA, shrinkB : float, default: 2

Shorten the arrow path at posA and posB by this amount in points. This allows to add a margin between the intended start/end points and the arrow.

Ignored if path is provided.

mutation_scale : float, default: 1

Value with which attributes of arrowstyle (e.g., head_length) will be scaled.

mutation_aspect : None or float, default: None

The height of the rectangle will be squeezed by this value before the mutation and the mutated box will be stretched by the inverse of it.

Other Parameters

**kwargs : `~matplotlib.patches.Patch properties`, optional: Here is a list of available .Patch properties:

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: unknown 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 color: :mpltype:color edgecolor or ec: :mpltype:color or None facecolor or fc: :mpltype:color or None figure: ~matplotlib.figure.Figure or ~matplotlib.figure.SubFigure fill: bool gid: str hatch: {'/', '\', '|', '-', '+', 'x', 'o', 'O', '.', '*'} hatch_linewidth: unknown in_layout: bool 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 zorder: float

In contrast to other patches, the default capstyle and joinstyle for FancyArrowPatch are set to "round".

Ancestors

matplotlib.patches.FancyArrowPatch
matplotlib.patches.Patch
matplotlib.artist.Artist

Methods

def do_3d_projection(self, renderer=None)

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def do_3d_projection(self, renderer=None):
    xs3d, ys3d, zs3d = self._verts3d
    xs, ys, zs = proj3d.proj_transform(xs3d, ys3d, zs3d, self.axes.M)
    self.set_positions((xs[0],ys[0]),(xs[1],ys[1]))

    return np.min(zs)

def set(self, *, agg_filter=<UNSET>, alpha=<UNSET>, animated=<UNSET>, antialiased=<UNSET>, arrowstyle=<UNSET>, capstyle=<UNSET>, clip_box=<UNSET>, clip_on=<UNSET>, clip_path=<UNSET>, color=<UNSET>, connectionstyle=<UNSET>, edgecolor=<UNSET>, facecolor=<UNSET>, fill=<UNSET>, gid=<UNSET>, hatch=<UNSET>, hatch_linewidth=<UNSET>, in_layout=<UNSET>, joinstyle=<UNSET>, label=<UNSET>, linestyle=<UNSET>, linewidth=<UNSET>, mouseover=<UNSET>, mutation_aspect=<UNSET>, mutation_scale=<UNSET>, patchA=<UNSET>, patchB=<UNSET>, path_effects=<UNSET>, picker=<UNSET>, positions=<UNSET>, rasterized=<UNSET>, sketch_params=<UNSET>, snap=<UNSET>, transform=<UNSET>, url=<UNSET>, visible=<UNSET>, zorder=<UNSET>)

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cls.set = lambda self, **kwargs: Artist.set(self, **kwargs)

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: float or None animated: bool antialiased or aa: bool or None arrowstyle: [ '-' | '<-' | '->' | '<->' | '<|-' | '-|>' | '<|-|>' | ']-' | '-[' | ']-[' | '|-|' | ']->' | '<-[' | 'simple' | 'fancy' | 'wedge' ] capstyle: .CapStyle or {'butt', 'projecting', 'round'} clip_box: ~matplotlib.transforms.BboxBase or None clip_on: bool clip_path: Patch or (Path, Transform) or None color: :mpltype:color connectionstyle: [ 'arc3' | 'angle3' | 'angle' | 'arc' | 'bar' ] edgecolor or ec: :mpltype:color or None facecolor or fc: :mpltype:color or None figure: ~matplotlib.figure.Figure or ~matplotlib.figure.SubFigure fill: bool gid: str hatch: {'/', '\', '|', '-', '+', 'x', 'o', 'O', '.', '*'} hatch_linewidth: unknown in_layout: bool joinstyle: .JoinStyle or {'miter', 'round', 'bevel'} label: object linestyle or ls: {'-', '–', '-.', ':', '', (offset, on-off-seq), …} linewidth or lw: float or None mouseover: bool mutation_aspect: float mutation_scale: float patchA: .patches.Patch patchB: .patches.Patch path_effects: list of .AbstractPathEffect picker: None or bool or float or callable positions: unknown rasterized: bool sketch_params: (scale: float, length: float, randomness: float) snap: bool or None transform: ~matplotlib.transforms.Transform url: str visible: bool zorder: float