def plot_gtf(panel: plt.Axes, data: list, y_offset: float,
linewidths: list) -> plt.Axes:
"""Apply gtf data to specified data axis."""
# initialize y_index
y_index = y_offset
# This dictionary is used to plot hte width based on type
lwdd = {
"transcript": linewidths[0],
"exon": linewidths[1],
"CDS": linewidths[2]
}
# This dictionary holds the last valued plotted at each y_index.
y_index_dict = {}
# Groups by each transcript ID
for _, group in groupby(data, itemgetter(0)):
# Convert from iterator to list.
group = list(group)
new_start = min([x[2] for x in group])
new_end = max([x[3] for x in group])
# set the y_index
if y_index_dict.keys():
y_index = max(y_index_dict.keys()) + y_offset
for dict_key in y_index_dict:
if new_start > y_index_dict[dict_key]:
y_index = min(dict_key, y_index)
for feature in group:
panel.add_patch(
mplpatches.Rectangle(xy=(feature[2],
(y_index - (lwdd[feature[1]] / 2))),
width=(feature[3] - feature[2]),
height=lwdd[feature[1]],
edgecolor=None,
facecolor='Black'))
y_index_dict[y_index] = new_end
return panel
def draw_bbox_rectangle(ax: plt.Axes, box: Bbox):
"""Draws a green rectangle around the specified Bbox"""
rect = Rectangle(xy=(box.x0, box.y0), width=box.width, height=box.height,
transform=ax.get_transform(), clip_on=False, color="green", fill=False)
rect.set_in_layout(False)
ax.add_patch(rect)
def _add_rectangle(
self,
axes: plt.Axes,
label: Optional[str],
rectangle_dims: Mapping[str, Union[float, Tuple[float, float]]],
alpha: float = 0.1,
):
"""Plot a rectangle on given coordinates around reaction forces.
Args:
forces_legend: the description of the forces that appears on the
legend.
rectangle_dims: a mapping that should have the following keys:
`"xy"`, `"width"`, `"height"`. The first should be the `(x_pos,
y_pos)` coordinates of the rectangle's bottom-left corner, the
other two single numbers.
box_legend: the description of the rectangle that appears on the
legend.
alpha: transparency of the rectangle.
kwargs: passed to :py:meth:`SegmentPlotter.plot_reactions`.
"""
rect = patches.Rectangle(**rectangle_dims, alpha=alpha, label=label)
axes.add_patch(rect)
def plot2axes(self,
axes: plt.Axes = None,
edgecolor: str = 'black',
fill: bool = False,
plot_peaks: bool = True):
"""Add 2 circles to the axes: one at the maximum and minimum radius of the ROI.
See Also
--------
:meth:`~pylinac.core.profile.CircleProfile.plot2axes` : Further parameter info.
"""
if axes is None:
fig, axes = plt.subplots()
axes.imshow(self.image_array)
axes.add_patch(
mpl_Circle((self.center.x, self.center.y),
edgecolor=edgecolor,
radius=self.radius * (1 + self.width_ratio),
fill=fill))
axes.add_patch(
mpl_Circle((self.center.x, self.center.y),
edgecolor=edgecolor,
radius=self.radius * (1 - self.width_ratio),
fill=fill))
if plot_peaks:
x_locs = [peak.x for peak in self.peaks]
y_locs = [peak.y for peak in self.peaks]
axes.autoscale(enable=False)
axes.scatter(x_locs, y_locs, s=20, marker='x', c=edgecolor)
def plot2axes(self,
axes: plt.Axes,
edgecolor: str = 'black',
angle: float = 0.0,
fill: bool = False,
alpha: float = 1,
facecolor: str = 'g'):
"""Plot the Rectangle to the axes.
Parameters
----------
axes : matplotlib.axes.Axes
An MPL axes to plot to.
edgecolor : str
The color of the circle.
angle : float
Angle of the rectangle.
fill : bool
Whether to fill the rectangle with color or leave hollow.
"""
axes.add_patch(
mpl_Rectangle((self.bl_corner.x, self.bl_corner.y),
width=self.width,
height=self.height,
angle=angle,
edgecolor=edgecolor,
alpha=alpha,
facecolor=facecolor,
fill=fill))
def __plot_bunches(self,
fig: plt.Figure,
ax: plt.Axes,
point: FiniteMetricVertex,
name: str = "u") -> None:
"""
Plot all points and highlight the bunches for the given point on
the provided figure/axes.
:param fig: The matplotlib figure to plot on.
:param ax: The matplotlib axes to plot on.
:param point: The vertex whose bunches we wish to plot.
:param name: The name to use to label the vertex/bunches.
"""
ax.cla()
# Plot all points and color by set A_i
ax.scatter([v.i for v in self.vertices], [v.j for v in self.vertices],
s=4,
color="black",
marker=".",
label="Points")
# Plot and label the point itself
ax.scatter([point.i], [point.j],
s=12,
color="red",
marker="*",
label=name)
ax.annotate(name, (point.i, point.j), color="red")
# Force the xlim and ylim to become fixed
ax.set_xlim(*ax.get_xlim())
ax.set_ylim(*ax.get_ylim())
# For the current point, mark and label its p_i s
# and add circles
p_i = [self.p[point][i] for i in range(self.k)]
for i in range(1, self.k):
if p_i[i] is None:
continue
ax.annotate("p_{}({})".format(i, name), (p_i[i][0].i, p_i[i][0].j),
xytext=(5, 5),
textcoords="offset pixels",
color="violet")
circ = plt.Circle((point.i, point.j), p_i[i][1], fill=False)
ax.add_patch(circ)
# Plot the points in the bunch
B = [w for w in self.B[point]]
ax.scatter([w.i for w in B], [w.j for w in B],
s=12,
color="lime",
marker="*",
label="B({})".format(name))
ax.set_title("Bunch B({})".format(name))
ax.legend(bbox_to_anchor=(1.05, 1.0), loc='upper left')
plt.tight_layout()
fig.show()
def plot2axes(self,
axes: plt.Axes = None,
edgecolor: str = 'black',
fill: bool = False,
plot_peaks: bool = True):
"""Plot the circle to an axes.
Parameters
----------
axes : matplotlib.Axes, None
The axes to plot on. If None, will create a new figure of the image array.
edgecolor : str
Color of the Circle; must be a valid matplotlib color.
fill : bool
Whether to fill the circle. matplotlib keyword.
plot_peaks : bool
If True, plots the found peaks as well.
"""
if axes is None:
fig, axes = plt.subplots()
axes.imshow(self.image_array)
axes.add_patch(
mpl_Circle((self.center.x, self.center.y),
edgecolor=edgecolor,
radius=self.radius,
fill=fill))
if plot_peaks:
x_locs = [peak.x for peak in self.peaks]
y_locs = [peak.y for peak in self.peaks]
axes.autoscale(enable=False)
axes.scatter(x_locs, y_locs, s=40, marker='x', c=edgecolor)
def plot_psl(panel: plt.Axes, data: list, y_offset: float,
linewidths: list) -> plt.Axes:
"""Apply psl data to specified data axis."""
# initialize the offset
y_index = y_offset
# Dict holds Y values and furthest right point of any line.
y_index_dict = {}
# checks to see if line overlaps other line(s) and sets y index accordingly
for _, record in enumerate(data):
if y_index_dict.keys():
y_index = max(y_index_dict.keys()) + y_offset
for dict_key in y_index_dict:
if record[1] > y_index_dict[dict_key]:
y_index = min(dict_key, y_index)
# Adds the main rectangle
panel.add_patch(
mplpatches.Rectangle(xy=(record[1], y_index),
width=record[2] - record[1],
height=linewidths[0],
edgecolor=None,
facecolor='Black'))
# Adds all the features of the main rectangle.
for feature in zip(record[3], record[4]):
panel.add_patch(
mplpatches.Rectangle(xy=(feature[0],
(y_index - (linewidths[1] / 2))),
width=feature[1],
height=linewidths[1],
edgecolor=None,
facecolor='Black'))
# updates dictionary
y_index_dict[y_index] = record[2]
return panel
def plot_radius_circle(fig: plt.Figure, ax: plt.Axes, R: PlanarTriangle,
P: Triangle, i: int):
sol = R.min_max_traversal_triangle(P)
circle = Circle(R.points[i],
np.linalg.norm(sol.points[i] - R.points[i]),
linestyle="--",
fill=None)
ax.add_patch(circle)
def draw_objects(axes: plt.Axes, objects: list):
for obj in objects:
x_bounds = obj.bounds['x']
y_bounds = obj.bounds['y']
x = x_bounds[0]
w = x_bounds[1] - x
y = y_bounds[0]
h = y_bounds[1] - y
axes.add_patch(patches.Rectangle((x, y), w, h, color='gray'))
def draw_path(self, ax: plt.Axes, path, properties: Properties, z: float):
vertices, codes = _get_path_patch_data(path)
patch = PathPatch(Path(vertices, codes),
linewidth=self.lineweight(properties),
linestyle=self.pattern(properties),
fill=False,
color=properties.color,
zorder=z)
ax.add_patch(patch)
def draw_segmentation(
img: np.ndarray,
mask: np.ndarray,
idx_name_dict: Dict[int, str],
colors: List = None,
title: str = '',
ax: plt.Axes = None,
figsize: Tuple[int, int] = (16, 8),
):
if colors is None:
colors = generate_colormap(len(idx_name_dict) + 1)
if ax is None:
_, ax = plt.subplots(figsize=figsize)
width, height = img.size
ax.set_ylim(height + 10, -10)
ax.set_xlim(-10, width + 10)
ax.axis('off')
ax.set_title(title)
out_image = np.array(img).astype(np.uint8)
for cat in np.unique(mask)[1:]:
mask_cat = (mask == cat)
cat_name = idx_name_dict[cat]
color = colors[cat]
# draw text in the center (defined by median) when box is not drawn
# median is less sensitive to outliers.
text_pos = np.median(mask_cat.nonzero(), axis=1)[::-1] - 20
# horiz_align = "left"
lighter_color = change_color_brightness(color, brightness_factor=0.7)
font_size = 10
draw_text(ax,
cat_name,
text_pos,
font_size,
horizontal_alignment='left')
padded_mask = np.zeros((mask_cat.shape[0] + 2, mask_cat.shape[1] + 2),
dtype=np.uint8)
padded_mask[1:-1, 1:-1] = mask_cat
contours = measure.find_contours(padded_mask, 0.5)
for verts in contours:
verts = np.fliplr(verts) - 1
p = Polygon(
verts,
facecolor=color,
edgecolor=lighter_color, # 'black',
fill=True,
alpha=.5)
ax.add_patch(p)
ax.imshow(out_image)
return ax
def plot_arrow(fig: plt.Figure, ax: plt.Axes, R: PlanarTriangle, P: Triangle,
i: int, scale: bool):
triv = get_triv(R, P, i)
length = triv.points[2] - R.points[i]
if scale:
length *= P.sides[(i + 1) % 3]
arrow = FancyArrow(*R.points[i],
*length,
length_includes_head=True,
head_width=0.035,
color="black")
ax.add_patch(arrow)
def __plot_p_i(self,
fig: plt.Figure,
ax: plt.Axes,
point: FiniteMetricVertex,
name: str = "u") -> None:
"""
Plot all points and highlight the witnesses p_i for the given point
along with corresponding rings on the given figure and axes.
:param fig: The matplotlib figure to plot on.
:param ax: The matplotlib axes to plot on.
:param point: The vertex whose witnesses/rings we wish to plot.
:param name: The name to use to label the vertex/bunches.
"""
ax.cla()
# Plot all points and color by set A_i
for i, a_i in enumerate(self.A):
ax.scatter([v.i for v in a_i], [v.j for v in a_i],
s=8,
marker="o",
label="A_{}".format(i))
# Plot and label the point itself
ax.scatter([point.i], [point.j],
s=12,
color="red",
marker="*",
label=name)
ax.annotate(name, (point.i, point.j), color="red")
# Force the xlim and ylim to become fixed
ax.set_xlim(*ax.get_xlim())
ax.set_ylim(*ax.get_ylim())
# For the current point, mark and label its p_i s
# and add circles
p_i = [self.p[point][i] for i in range(self.k)]
for i in range(1, self.k):
if p_i[i] is None:
continue
ax.annotate("p_{}({})".format(i, name), (p_i[i][0].i, p_i[i][0].j),
xytext=(5, 5),
textcoords="offset pixels",
color="violet")
circ = plt.Circle((point.i, point.j), p_i[i][1], fill=False)
ax.add_patch(circ)
ax.set_title("Witnesses p_i({}) and rings.".format(name))
ax.legend(bbox_to_anchor=(1.05, 1.0), loc='upper left')
plt.tight_layout()
fig.show()
def plot_bb_image(image: np.ndarray,
bbs: List[List[float]] = [],
relative_size_bb=True,
ax: plt.Axes = None):
"""
Plot an image and a set of bounding boxes.
:param image: The image as a numpy array
:param bbs: A list of lists, which inner list having five values. The first one being the class and then
[xmin, xmax, ymin, ymax]
:param relative_size_bb: When True the bounding boxes are assumed to be relative to the size of the image. So
values between 0 and 1.
:param ax: A plt.Axes object where to plot the image and bounding boxes when required. If not passed, it will create
one.
:return: None.
"""
pass_ax = True
if ax is None:
pass_ax = False
# Create figure and axes
fig, ax = plt.subplots(1)
# Display the image
ax.imshow(image.astype(np.uint8))
h, w = image.shape[:2]
sizes = [w, h, w, h]
colors = ['r', 'g', 'b', 'k']
for bb in bbs:
label = bb[0]
color = colors[label]
if relative_size_bb:
#Convert bounding boxes from relative to absolute values
bb = [
int(round(size * coord)) for coord, size in zip(bb[1:], sizes)
]
# Create a Rectangle patch
rect = patches.Rectangle((bb[0], bb[1]),
bb[2] - bb[0],
bb[3] - bb[1],
linewidth=2,
edgecolor=color,
facecolor='none')
# Add the patch to the Axes
ax.add_patch(rect)
if not pass_ax:
plt.axis('off')
plt.show()
def __init__(
self, *points, ax: plt.Axes = None, color=grey_dark, **kwargs,
):
"""
Given a list of tuples/lists of XY coordinates of each point,
this class draws a polygon
"""
ax = ax or plt.gca()
xy = np.vstack(points)
patch = Polygon_patch(xy, color=color, **kwargs)
ax.add_patch(patch)
def plot_init(self, ax: plt.Axes):
"""Copied from https://matplotlib.org/3.1.1/gallery/animation/animated_histogram.html"""
import matplotlib.patches as patches
import matplotlib.path as path
self.artists = []
ax.clear()
_apply_hook(ax, self.hook)
init_data = self.data.flatten()
n, bins = np.histogram(init_data, self.num_bins)
# get the corners of the rectangles for the histogram
left = np.array(bins[:-1])
right = np.array(bins[1:])
self._bottom = np.zeros(len(left))
top = self._bottom + n / (self.num_frames * 0.9)
nrects = len(left)
# here comes the tricky part -- we have to set up the vertex and path
# codes arrays using moveto, lineto and closepoly
# for each rect: 1 for the MOVETO, 3 for the LINETO, 1 for the
# CLOSEPOLY; the vert for the closepoly is ignored but we still need
# it to keep the codes aligned with the vertices
nverts = nrects * (1 + 3 + 1)
self._verts = np.zeros((nverts, 2))
codes = np.ones(nverts, int) * path.Path.LINETO
codes[0::5] = path.Path.MOVETO
codes[4::5] = path.Path.CLOSEPOLY
self._verts[0::5, 0] = left
self._verts[1::5, 0] = left
self._verts[2::5, 0] = right
self._verts[3::5, 0] = right
self._verts[1::5, 1] = top
self._verts[2::5, 1] = top
self._verts[0::5, 1] = self._bottom
self._verts[3::5, 1] = self._bottom
barpath = path.Path(self._verts, codes)
patch = patches.PathPatch(barpath, facecolor="green", edgecolor="yellow", alpha=0.5)
ax.add_patch(patch)
ax.set_xlim(left[0], right[-1])
ax.set_ylim(self._bottom.min(), top.max())
self.artists.append(patch)
def __init__(
self,
x_0,
x_1,
y_0,
y_1,
ax: plt.Axes = None,
color=blue_grey_dark,
**kwargs,
):
ax = ax or plt.gca()
rect = Rectangle_patch(
(x_0, y_0), x_1 - x_0, y_1 - y_0, color=color, **kwargs
)
ax.add_patch(rect)
def plot_cube_2D(ax: plt.Axes, cube: Cube):
"""Plots the :class:`Rubix Cube <Cube>` on a
:class:`matplotlib Axes <matplotlib.axes.Axes>` on a flattened 2-D
representation.
Args:
ax (plt.Axes): The :class:`matplotlib Axes <matplotlib.axes.Axes>`
on which the plotting will be done.
cube (Cube): :class:`Rubix Cube <Cube>` that will be plotted in a
flattened 2-D representation of all 6 sides.
Returns:
None.
"""
# Ensures the arguments are well-formed.
if cube.is_well_formed()\
and isinstance(ax , plt.Axes):
for face_name in cube.faces:
# Grabs the local coordinates for each face
face_local_coords = FACE_COORDS[face_name]
# Grabs the face values for filling in the plot for each tile
# in the 2-D representation.
face_values = cube.faces[face_name]
#print(f"{face_name} : ")
for row_idx, row in enumerate(face_values):
for col_idx, color_val in enumerate(row):
tile_coords = (face_local_coords[0] + 100 * col_idx,
face_local_coords[1] - 100 * row_idx)
#print(f"\t[{row_idx},{col_idx}] : {tile_coords}")
rect = patches.Rectangle(xy=tile_coords,
width=100,
height=100,
facecolor=str(color_val),
lw=2,
edgecolor='black')
ax.add_patch(rect)
def draw_ellipse(position: List[float],
covariance: List[float],
ax: plt.Axes = None):
"""Draw an ellipse with a given position and covariance"""
angle = 0
width, height = 2 * np.sqrt(covariance)
# Draw the Ellipse
for n in range(1, 4):
ax.add_patch(
Ellipse(position,
n * width,
n * height,
angle,
alpha=1 / (width + height),
color='red'))
def _plot_ellipse_covariance(mean,
cov,
ax: plt.Axes,
confidence=.9,
facecolor='none',
edgecolor="k",
linestyle='--',
**kwargs):
if type(confidence) is not list:
confidence = [confidence]
eigvals, eigvecs = np.linalg.eigh(cov)
if np.min(eigvals) < 0:
print(f"Found a negative eigenvalue. Aborting. ({eigvals})")
return
eigvals = np.sqrt(eigvals)
if eigvecs[1, 0] == 0:
angle = np.sign(eigvecs[1, 1]) * 90
else:
angle = np.arctan(eigvecs[1, 1] / eigvecs[1, 0]) * 360 / (2 * np.pi)
patches = []
for conf in confidence:
s = np.sqrt(chi2.ppf(conf, df=2))
ellipse = Ellipse(mean,
width=2 * eigvals[1] * s,
height=2 * eigvals[0] * s,
angle=angle,
facecolor=facecolor,
alpha=.3,
edgecolor=edgecolor,
linestyle=linestyle,
**kwargs)
patches.append(ax.add_patch(ellipse))
return patches
def _draw_rect(ax:plt.Axes, b:Collection[int], color:str='white', text=None, text_size=14):
"Draw bounding box on `ax`."
patch = ax.add_patch(patches.Rectangle(b[:2], *b[-2:], fill=False, edgecolor=color, lw=2))
_draw_outline(patch, 4)
if text is not None:
patch = ax.text(*b[:2], text, verticalalignment='top', color=color, fontsize=text_size, weight='bold')
_draw_outline(patch,1)
def plot_cov_ellipse2d(
ax: plt.Axes,
mean: np.ndarray = np.zeros(2),
cov: np.ndarray = np.eye(2),
n_sigma: float = 1,
*,
edgecolor: "Color" = "C0",
facecolor: "Color" = "none",
**kwargs, # extra Ellipse keyword arguments
) -> matplotlib.patches.Ellipse:
"""Plot a n_sigma covariance ellipse centered in mean into ax."""
ell_trans_mat = np.zeros((3, 3))
ell_trans_mat[:2, :2] = np.linalg.cholesky(cov)
ell_trans_mat[:2, 2] = mean
ell_trans_mat[2, 2] = 1
ell = matplotlib.patches.Ellipse(
(0.0, 0.0),
2.0 * n_sigma,
2.0 * n_sigma,
edgecolor=edgecolor,
facecolor=facecolor,
**kwargs,
)
trans = matplotlib.transforms.Affine2D(ell_trans_mat)
ell.set_transform(trans + ax.transData)
return ax.add_patch(ell)
def plot_cov_ellipse2d(
ax: plt.Axes = None,
mean: np.ndarray = np.zeros(2),
cov: np.ndarray = np.eye(2),
n_sigma: float = 1,
*,
edgecolor: Color = 'C0',
facecolor: Color = 'none',
**kwargs, # other Ellipse keyword arguments
) -> Optional[Ellipse]:
"""Plot a n_sigma covariance ellipse centered in mean into ax."""
if ax is None:
ax = plt.gca()
if mean is None or cov is None:
print('None parameters not handled: ellipse not plotted')
return
ell_trans_mat = np.zeros((3, 3))
ell_trans_mat[:2, :2] = np.linalg.cholesky(cov)
ell_trans_mat[:2, 2] = mean
ell_trans_mat[2, 2] = 1
ell = Ellipse((0.0, 0.0),
2.0 * n_sigma,
2.0 * n_sigma,
edgecolor=edgecolor,
facecolor=facecolor,
**kwargs)
trans = Affine2D(ell_trans_mat)
ell.set_transform(trans + ax.transData)
return ax.add_patch(ell)
def alpha_label(
axes_: Axes,
xy_pt1_B: np.ndarray,
xy_pt2_B: np.ndarray,
color_: str = red_,
) -> None:
label_xy = [0.55, 0.75]
axes_.text(
*label_xy,
r"$-\alpha$",
color=color_,
fontsize=20,
rotation=0,
transform=axes_.transAxes,
horizontalalignment="center",
verticalalignment="center",
)
# angle_ref = 0
angle_B = np.rad2deg(
np.arctan(
(xy_pt2_B[1] - xy_pt1_B[1])
/ (xy_pt2_B[0] - xy_pt1_B[0])
)
)
radius = 0.88
axes_.add_patch(
Arc(
xy_pt2_B,
radius,
radius,
color=color_,
linestyle="--",
linewidth=2,
fill=False,
zorder=2,
# transform=axes_.transAxes,
angle=angle_B,
theta1=0,
theta2=-angle_B,
)
)
axes_.plot(
[xy_pt2_B[0], xy_pt2_B[0] + 0.5],
[xy_pt2_B[1], xy_pt2_B[1]],
":",
color=color_,
)
def psi_label(
axes_: Axes,
xy_pt1_B: np.ndarray,
xy_pt2_B: np.ndarray,
xy_pt1_C: np.ndarray,
xy_pt2_C: np.ndarray,
color_: str = red_,
) -> None:
label_xy = [0.5, 0.53]
axes_.text(
*label_xy,
r"$\psi$",
color=color_,
fontsize=20,
rotation=0,
transform=axes_.transAxes,
horizontalalignment="center",
verticalalignment="center",
)
angle_B = np.rad2deg(
np.arctan(
(xy_pt2_B[1] - xy_pt1_B[1])
/ (xy_pt2_B[0] - xy_pt1_B[0])
)
)
angle_C = np.rad2deg(
np.arctan(
(xy_pt2_C[1] - xy_pt1_C[1])
/ (xy_pt2_C[0] - xy_pt1_C[0])
)
)
radius = 0.95
axes_.add_patch(
Arc(
xy_pt2_B,
radius,
radius,
color=color_,
linewidth=2,
fill=False,
zorder=2,
# transform=axes_.transAxes,
angle=angle_B,
theta1=0,
theta2=angle_C - angle_B,
)
)
def drawRect(ax: plt.Axes,
x0: float,
y0: float,
x1: float,
y1: float,
color=None,
alpha: float = None,
edgecolor=None,
label: str = None,
profile: dict = None) -> None:
"""
Draw a rectangle from point (x0, y0) to (x1, y1)
Args:
ax: the plot axe
x0: x coord of the start point
y0: y coord of the start point
x1: x coord of the end point
y1: y coord of the end point
color: the face color
edgecolor: the color of the edges
alpha: alpha value for the rectangle (both facecolor and edgecolor)
label: if given, a label is plotted at the center of the rectangle
profile: the profile used, or None for default
"""
facecolor = _fallback(color, profile, 'facecolor')
edgecolor = _fallback(edgecolor, profile, 'edgecolor')
facecolor = _getcolor(facecolor)
edgecolor = _getcolor(edgecolor)
alpha = alpha if alpha is not None else _get(profile, 'alpha')
rect = Rectangle((x0, y0),
x1 - x0,
y1 - y0,
facecolor=facecolor,
edgecolor=edgecolor,
alpha=alpha)
ax.add_patch(rect)
if label is not None:
drawLabel(ax,
x=(x0 + x1) * 0.5,
y=(y0 + y1) * 0.5,
text=label,
profile=profile)
if _get(profile, 'autoscale'):
autoscaleAxis(ax)
def draw(self, ax: plt.Axes, show_range: bool = False):
"""Draw boid on provided matplotlib axes object.
:param ax: axes on which the boid should be drawn.
:param show_range: whether to also show "seeing" range of the boid.
"""
if show_range:
arc = ptch.Arc(
(self.x, self.y),
width=2 * self.lu_distance,
height=2 * self.lu_distance,
angle=math.degrees(self.direction),
theta1=math.degrees(2 * math.pi - self.lu_angle / 2),
theta2=math.degrees(self.lu_angle / 2),
color='black',
linewidth=1,
alpha=0.3,
zorder=5)
line_1 = plt.Line2D([
self.x + self.lu_distance *
math.cos(self.lu_angle / 2 + self.direction), self.x
], [
self.y + self.lu_distance *
math.sin(self.lu_angle / 2 + self.direction), self.y
],
color='black',
linewidth=1,
alpha=0.3,
zorder=5)
line_2 = plt.Line2D([
self.x + self.lu_distance *
math.cos(2 * math.pi - self.lu_angle / 2 + self.direction),
self.x
], [
self.y + self.lu_distance *
math.sin(2 * math.pi - self.lu_angle / 2 + self.direction),
self.y
],
color='black',
linewidth=1,
alpha=0.3,
zorder=5)
ax.add_line(line_1)
ax.add_line(line_2)
ax.add_patch(arc)
ax.add_patch(self._arrow_representation())
def add_internal_window_to_subplot(sampled: samples.Samples,
ax: plt.Axes) -> None:
if ax is None:
return
loss_window_radius = sampled.config.data_build.loss_window_radius
window_radius = sampled.config.data_build.window_radius
if loss_window_radius == window_radius:
return
buffer = int(window_radius - loss_window_radius)
rect = patches.Rectangle((buffer, buffer),
loss_window_radius * 2,
loss_window_radius * 2,
linewidth=1,
edgecolor="red",
facecolor="none")
ax.add_patch(rect)
def patch_chance_level(level=None,
signs=(-1, 1),
ax: plt.Axes = None,
xy='y',
color=(0.7, 0.7, 0.7)):
if level is None:
level = np.log(10.)
if ax is None:
ax = plt.gca()
hs = []
for sign in signs:
if xy == 'y':
if ax.yaxis.get_scale() == 'log':
vmin = 1.
level1 = level * 10**sign
else:
vmin = 0.
level1 = level * sign
lim = ax.get_xlim()
rect = mpl.patches.Rectangle([lim[0], vmin],
lim[1] - lim[0],
level1,
linewidth=0,
fc=color,
zorder=-1)
elif xy == 'x':
if ax.xaxis.get_scale() == 'log':
vmin = 1.
level1 = level * 10**sign
else:
vmin = 0.
level1 = level * sign
lim = ax.get_ylim()
rect = mpl.patches.Rectangle([vmin, lim[0]],
level1,
lim[1] - lim[0],
linewidth=0,
fc=color,
zorder=-1)
ax.add_patch(rect)
hs.append(rect)
return hs
def plot2axes(self, axes: plt.Axes=None, edgecolor: str='black', fill: bool=False, plot_peaks: bool=True):
"""Add 2 circles to the axes: one at the maximum and minimum radius of the ROI.
See Also
--------
:meth:`~pylinac.core.profile.CircleProfile.plot2axes` : Further parameter info.
"""
if axes is None:
fig, axes = plt.subplots()
axes.imshow(self.image_array)
axes.add_patch(mpl_Circle((self.center.x, self.center.y), edgecolor=edgecolor, radius=self.radius*(1+self.width_ratio),
fill=fill))
axes.add_patch(mpl_Circle((self.center.x, self.center.y), edgecolor=edgecolor, radius=self.radius*(1-self.width_ratio),
fill=fill))
if plot_peaks:
x_locs = [peak.x for peak in self.peaks]
y_locs = [peak.y for peak in self.peaks]
axes.autoscale(enable=False)
axes.scatter(x_locs, y_locs, s=20, marker='x', c=edgecolor)
def plot2axes(self, axes: plt.Axes, edgecolor: str='black', angle: float=0.0, fill: bool=False,
alpha: float=1, facecolor: str='g'):
"""Plot the Rectangle to the axes.
Parameters
----------
axes : matplotlib.axes.Axes
An MPL axes to plot to.
edgecolor : str
The color of the circle.
angle : float
Angle of the rectangle.
fill : bool
Whether to fill the rectangle with color or leave hollow.
"""
axes.add_patch(mpl_Rectangle((self.bl_corner.x, self.bl_corner.y),
width=self.width,
height=self.height,
angle=angle,
edgecolor=edgecolor,
alpha=alpha,
facecolor=facecolor,
fill=fill))
def plot2axes(self, axes: plt.Axes=None, edgecolor: str='black', fill: bool=False, plot_peaks: bool=True):
"""Plot the circle to an axes.
Parameters
----------
axes : matplotlib.Axes, None
The axes to plot on. If None, will create a new figure of the image array.
edgecolor : str
Color of the Circle; must be a valid matplotlib color.
fill : bool
Whether to fill the circle. matplotlib keyword.
plot_peaks : bool
If True, plots the found peaks as well.
"""
if axes is None:
fig, axes = plt.subplots()
axes.imshow(self.image_array)
axes.add_patch(
mpl_Circle((self.center.x, self.center.y), edgecolor=edgecolor, radius=self.radius, fill=fill))
if plot_peaks:
x_locs = [peak.x for peak in self.peaks]
y_locs = [peak.y for peak in self.peaks]
axes.autoscale(enable=False)
axes.scatter(x_locs, y_locs, s=40, marker='x', c=edgecolor)
