def annotate_points_with_images(ax: plt.axes, indices: Union[List[int], np.ndarray],
plot_data: np.ndarray, image_data: np.ndarray,
image_size: Tuple[int, int],
xybox: Tuple[float, float] = (-40., 40.)) -> None:
"""
Annotates a plot of points with converted image data.
:param ax: A matplotlib axes object
:param indices: A list of indices to index image data and plot data.
:param plot_data: A 2D projection of image data.
:param image_data: Original image data, where each row corresponds to an array of image
data.
:param image_size: A tuple representing image size in pixels.
:return: None
"""
for i in indices:
ab = AnnotationBbox(
OffsetImage(
image_data[i, :].reshape(image_size[0], image_size[1]),
zoom=.8,
cmap='gray'
),
tuple(plot_data[i, :]),
xybox=xybox,
xycoords='data',
boxcoords="offset points",
pad=0.3,
arrowprops=dict(arrowstyle="->"))
ax.add_artist(ab)
def plot_cov(ax: plt.axes, mean: np.ndarray, cov_matrix: np.ndarray,
color: str) -> None:
# Helper function to visualize the distribution
vals, vecs = np.linalg.eigh(cov_matrix)
x, y = vecs[:, 0]
theta = np.degrees(np.arctan2(y, x))
w, h = 2 * np.sqrt(vals)
ax.add_artist(Ellipse(mean, w, h, theta, color=color, alpha=0.3))
def update_main_axes(axes: plt.axes, inside_circle: np.ndarray,
outside_circle: np.ndarray, circle: plt.Circle,
square: plt.Rectangle) -> None:
"""
Updates the main axes with the new information prior to taking a snapshot.
"""
axes.scatter(*(outside_circle.T), c="red", marker='.')
axes.scatter(*(inside_circle.T), c="green", marker='.')
axes.add_artist(circle)
axes.add_artist(square)
def draw_one_situation(self,
data: Data,
calibration: CalibData,
ax: plt.axes,
vmax=None,
vmin=None,
title_prefix=""):
"""
Draw one situation with object on the graph.
Args:
data: Data object to be visualized
calibration: CalibData object used for calibration
ax: matplotlib.pyplot.axes object
vmax: max value limit of the graph
vmin: min value limit of the graph
title_prefix: prefix for graph title
Returns:
im: matplotlib.image object
"""
obj = data
obj.calc_delta_V(calibration)
print(obj.x, obj.y, obj.z)
capacitance = self.solver.solve(obj.delta_V)
e_x, e_y, _ = self.get_COP(obj)
im = self.solver.plot_map_in_detection_range(ax,
capacitance,
vmax=vmax,
vmin=vmin)
circle = plt.Circle((obj.x, obj.y), 13.5, color='#F55400', fill=False)
circle_e = plt.Circle((e_x * 2000, e_y * 2000),
13.5,
color='k',
fill=False)
ax.set_xlim(-100, 100)
ax.set_ylim(-100, 100)
ax.add_artist(circle)
ax.add_artist(circle_e)
ax.set_title(title_prefix + "(" +
",".join((str(obj.x), str(obj.y), str(obj.z))) + ")")
ax.set_aspect('equal')
return im
def plot_gene_body(
ax: plt.axes,
gene: Mapping[str, Any],
gene_model_height: float,
vertical_offset: float = 0,
) -> None:
"""
Parameters
----------
ax
gene
gene_model_height
vertical_offset
Returns
-------
"""
gene_model_y = -gene_model_height + vertical_offset
gene_rect = patches.Rectangle(
xy=(1, gene_model_y),
width=gene["length"],
height=gene_model_height,
facecolor="white",
edgecolor="black",
linewidth=1,
)
ax.add_artist(gene_rect)
if "domains" in gene:
for domain in gene["domains"]:
domain_width = domain["end"] - domain["start"] + 1
rect = patches.Rectangle(
xy=(domain["start"], gene_model_y),
width=domain_width,
height=gene_model_height,
facecolor=domain["color"],
edgecolor="black",
linewidth=1,
)
ax.add_artist(rect)
ax.annotate(
s=domain["name"],
xy=(
domain["start"] + domain_width / 2,
gene_model_y + gene_model_height / 2,
),
ha="center",
va="center",
color=domain["textcolor"],
)
if "endlabels" in gene:
for endlabel in gene["endlabels"]:
# spacing = gene["length"] * 0.01 # TODO: fix so that the labels match up across multiple gene models
spacing = 10
if endlabel["side"] == "left":
endlabel_x = -spacing
endlabel_ha = "right"
elif endlabel["side"] == "right":
endlabel_x = gene["length"] + spacing
endlabel_ha = "left"
else:
raise ValueError("endlabel side must be one of 'left' or 'right'")
ax.annotate(
s=endlabel["text"],
xy=(endlabel_x, gene_model_y + gene_model_height / 2),
ha=endlabel_ha,
va="center",
color=endlabel["textcolor"],
)