def add_custom_ticks(ax: plt.Axes, tick_interp: np.ndarray):
# I'm playing some tricks here, and just relabeling the ticks on the x-axis
xticks = np.array(ax.get_xticks(), dtype=np.int)
# This catch is necessary because sometimes the last tick is out of bonds for our
# interpreted temp data
if xticks[-1] > tick_interp[-1].size:
xticks = xticks[:-1]
ax.set_xticklabels(["{:.0f}".format(t) for t in tick_interp[xticks]])
def update_disc_plot(ax: plt.Axes, d_x, d_g_z, update_interval):
clear_line(ax, 'dx')
clear_line(ax, 'dgz')
x = np.arange(1, len(d_x) + 1)
ax.plot(x, d_x, color='#308862', label='D(x)', gid='dx')
ax.plot(x, d_g_z, color='#B23F62', label='D(G(z))', gid='dgz', alpha=0.9)
ax.legend(loc='upper right', framealpha=0.75, bbox_to_anchor=(1.008, 1.136), ncol=5)
ax.set_xlim(left=1, right=len(x) + 0.01)
ax.set_ylim(0, 1.0)
ax.set_yticks(np.arange(0, 1, 0.1))
ticks = ax.get_xticks()
ax.set_xticklabels([f'{t:.0f}' for t in ticks * update_interval])
def update_loss_plot(ax: plt.Axes, d_loss, d_fake_loss, g_loss, update_interval, separate=False):
clear_line(ax, 'd_loss')
clear_line(ax, 'g_loss')
x = np.arange(1, len(d_loss) + 1)
if separate:
ax.plot(x, np.add(d_loss, d_fake_loss), color='dodgerblue', label='D Loss', gid='d_loss')
clear_line(ax, 'd_real_loss')
ax.plot(x, d_loss, color='lightseagreen', label='D Loss(Real)', gid='d_real_loss')
clear_line(ax, 'd_fake_loss')
ax.plot(x, d_fake_loss, color='mediumpurple', label='D Loss(Fake)', gid='d_fake_loss')
else:
ax.plot(x, d_loss, color='dodgerblue', label='D Loss', gid='d_loss')
ax.plot(x, g_loss, color='coral', label='G Loss', gid='g_loss', alpha=0.9)
ax.legend(loc='upper right', framealpha=0.75, bbox_to_anchor=(1.008, 1.136), ncol=5)
ax.set_xlim(left=1, right=len(x) + 0.01)
ticks = ax.get_xticks()
ax.set_xticklabels([f'{t:.0f}' for t in ticks * update_interval])
def add_percent_axis(ax: plt.Axes, data_size, flip_axis: bool = False) -> plt.Axes:
"""
Adds a twin axis with percentages to a count plot.
Args:
ax: Plot axes figure to add percentage axis to
data_size: Total count to use to normalize percentages
flip_axis: Whether the countplot had its axes flipped
Returns:
Twin axis that percentages were added to
"""
if flip_axis:
ax_perc = ax.twiny()
ax_perc.set_xticks(100 * ax.get_xticks() / data_size)
ax_perc.set_xlim(
(
100.0 * (float(ax.get_xlim()[0]) / data_size),
100.0 * (float(ax.get_xlim()[1]) / data_size),
)
)
ax_perc.xaxis.set_major_formatter(mtick.PercentFormatter())
ax_perc.xaxis.set_tick_params(labelsize=10)
else:
ax_perc = ax.twinx()
ax_perc.set_yticks(100 * ax.get_yticks() / data_size)
ax_perc.set_ylim(
(
100.0 * (float(ax.get_ylim()[0]) / data_size),
100.0 * (float(ax.get_ylim()[1]) / data_size),
)
)
ax_perc.yaxis.set_major_formatter(mtick.PercentFormatter())
ax_perc.yaxis.set_tick_params(labelsize=10)
ax_perc.grid(False)
return ax_perc
def draw_categorical(
plot_type: str,
ax: plt.Axes,
data: Union[list, np.ndarray, to.Tensor, pd.DataFrame],
x_label: Optional[Union[str, Sequence[str]]],
y_label: Optional[str],
vline_level: float = None,
vline_label: str = "approx. solved",
palette=None,
title: str = None,
show_legend: bool = True,
legend_kwargs: dict = None,
plot_kwargs: dict = None,
) -> plt.Figure:
"""
Create a box or violin plot for a list of data arrays or a pandas DataFrame.
The plot is neither shown nor saved.
If you want to order the 4th element to the 2nd position in terms of colors use
.. code-block:: python
palette.insert(1, palette.pop(3))
.. note::
If you want to have a tight layout, it is best to pass axes of a figure with `tight_layout=True` or
`constrained_layout=True`.
:param plot_type: tye of categorical plot, pass box or violin
:param ax: axis of the figure to plot on
:param data: list of data sets to plot as separate boxes
:param x_label: labels for the categories on the x-axis, if `data` is not given as a `DataFrame`
:param y_label: label for the y-axis, pass `None` to set no label
:param vline_level: if not `None` (default) add a vertical line at the given level
:param vline_label: label for the vertical line
:param palette: seaborn color palette, pass `None` to use the default palette
:param show_legend: if `True` the legend is shown, useful when handling multiple subplots
:param title: title displayed above the figure, set to None to suppress the title
:param legend_kwargs: keyword arguments forwarded to pyplot's `legend()` function, e.g. `loc='best'`
:param plot_kwargs: keyword arguments forwarded to seaborn's `boxplot()` or `violinplot()` function
:return: handle to the resulting figure
"""
plot_type = plot_type.lower()
if plot_type not in ["box", "violin"]:
raise pyrado.ValueErr(given=plot_type, eq_constraint="box or violin")
if not isinstance(data, (list, to.Tensor, np.ndarray, pd.DataFrame)):
raise pyrado.TypeErr(
given=data,
expected_type=[list, to.Tensor, np.ndarray, pd.DataFrame])
# Set defaults which can be overwritten
plot_kwargs = merge_dicts([dict(alpha=1),
plot_kwargs]) # by default no transparency
alpha = plot_kwargs.pop(
"alpha") # can't pass the to the seaborn plotting functions
legend_kwargs = dict() if legend_kwargs is None else legend_kwargs
palette = sns.color_palette() if palette is None else palette
# Preprocess
if isinstance(data, pd.DataFrame):
df = data
else:
if isinstance(data, list):
data = np.array(data)
elif isinstance(data, to.Tensor):
data = data.detach().cpu().numpy()
if x_label is not None and not len(x_label) == data.shape[1]:
raise pyrado.ShapeErr(given=data, expected_match=x_label)
df = pd.DataFrame(data, columns=x_label)
if data.shape[0] < data.shape[1]:
print_cbt(
f"Less data samples {data.shape[0]} then data dimensions {data.shape[1]}",
"y",
bright=True)
# Plot
if plot_type == "box":
ax = sns.boxplot(data=df, ax=ax, **plot_kwargs)
elif plot_type == "violin":
plot_kwargs = merge_dicts([
dict(alpha=0.3, scale="count", inner="box", bw=0.3, cut=0),
plot_kwargs
])
ax = sns.violinplot(data=df, ax=ax, palette=palette, **plot_kwargs)
# Plot larger circles for medians (need to memorize the limits)
medians = df.median().to_numpy()
left, right = ax.get_xlim()
locs = ax.get_xticks()
ax.scatter(locs,
medians,
marker="o",
s=30,
zorder=3,
color="white",
edgecolors="black")
ax.set_xlim((left, right))
# Postprocess
if alpha < 1 and plot_type == "box":
for patch in ax.artists:
r, g, b, a = patch.get_facecolor()
patch.set_facecolor((r, g, b, alpha))
elif alpha < 1 and plot_type == "violin":
for violin in ax.collections[::2]:
violin.set_alpha(alpha)
if vline_level is not None:
# Add dashed line to mark a threshold
ax.axhline(vline_level, c="k", ls="--", lw=1.0, label=vline_label)
if x_label is None:
ax.get_xaxis().set_ticks([])
if y_label is not None:
ax.set_ylabel(y_label)
if show_legend:
ax.legend(**legend_kwargs)
if title is not None:
ax.set_title(title)
return plt.gcf()
def break_axis(
amin,
amax=None,
xy='x',
ax: plt.Axes = None,
fun_draw: Callable = None,
margin=0.05,
) -> (plt.Axes, plt.Axes):
"""
:param amin: data coordinate to start breaking from
:param amax: data coordinate to end breaking at
:param xy: 'x' or 'y'
:param fun_draw: if not None, fun_draw(ax1) and fun_draw(ax2) will
be run to recreate ax. Use the same function as that was called for
with ax. Use, e.g., fun_draw=lambda ax: ax.plot(x, y)
:return: axs: a list of axes created
"""
if amax is None:
amax = amin
if ax is None:
ax = plt.gca()
if xy == 'x':
rect = ax.get_position().bounds
lim = ax.get_xlim()
prop_min = (amin - lim[0]) / (lim[1] - lim[0])
prop_max = (amax - lim[0]) / (lim[1] - lim[0])
rect1 = np.array([rect[0], rect[1], rect[2] * prop_min, rect[3]])
rect2 = [
rect[0] + rect[2] * prop_max, rect[1], rect[2] * (1 - prop_max),
rect[3]
]
fig = ax.figure # type: plt.Figure
ax1 = fig.add_axes(plt.Axes(fig=fig, rect=rect1))
ax1.update_from(ax)
if fun_draw is not None:
fun_draw(ax1)
ax1.set_xticks(ax.get_xticks())
ax1.set_xlim(lim[0], amin)
ax1.spines['right'].set_visible(False)
ax2 = fig.add_axes(plt.Axes(fig=fig, rect=rect2))
ax2.update_from(ax)
if fun_draw is not None:
fun_draw(ax2)
ax2.set_xticks(ax.get_xticks())
ax2.set_xlim(amax, lim[1])
ax2.spines['left'].set_visible(False)
ax2.set_yticks([])
ax.set_visible(False)
# plt.show() # CHECKED
axs = [ax1, ax2]
elif xy == 'y':
rect = ax.get_position().bounds
lim = ax.get_ylim()
prop_all = ((amin - lim[0]) + (lim[1] - amax)) / (1 - margin)
prop_min = (amin - lim[0]) / prop_all
prop_max = (lim[1] - amax) / prop_all
rect1 = np.array([rect[0], rect[1], rect[2], rect[3] * prop_min])
rect2 = [
rect[0], rect[1] + rect[3] * (1 - prop_max), rect[2],
rect[3] * (1 - prop_max)
]
fig = ax.figure # type: plt.Figure
ax1 = fig.add_axes(plt.Axes(fig=fig, rect=rect1))
ax1.update_from(ax)
if fun_draw is not None:
fun_draw(ax1)
ax1.set_yticks(ax.get_yticks())
ax1.set_ylim(lim[0], amin)
ax1.spines['top'].set_visible(False)
ax2 = fig.add_axes(plt.Axes(fig=fig, rect=rect2))
ax2.update_from(ax)
if fun_draw is not None:
fun_draw(ax2)
ax2.set_yticks(ax.get_yticks())
ax2.set_ylim(amax, lim[1])
ax2.spines['bottom'].set_visible(False)
ax2.set_xticks([])
ax.set_visible(False)
# plt.show() # CHECKED
axs = [ax1, ax2]
else:
raise ValueError()
return axs
def cases_and_deaths(
data: pd.DataFrame,
dates: bool = False,
ax: plt.Axes = None,
smooth: bool = True,
cases: str = "cases",
deaths: str = "deaths",
tight_layout=False,
**kwargs,
) -> plt.Axes:
"""
A simple chart showing observed new cases cases as vertical bars and
a smoothed out prediction of this curve.
Args:
data:
A dataframe with ["cases", "deaths"] columns.
dates:
If True, show dates instead of days in the x-axis.
ax:
An explicit matplotlib axes.
smooth:
If True, superimpose a plot of a smoothed-out version of the cases
curve.
cases:
deaths:
Name of the cases/deaths columns in the dataframe.
"""
if not dates:
data = data.reset_index(drop=True)
# Smoothed data
col_names = {cases: _("Cases"), deaths: _("Deaths")}
if smooth:
from pydemic import fitting as fit
smooth = pd.DataFrame(
{
_("{} (smooth)").format(col_names[cases]):
fit.smoothed_diff(data[cases]),
_("{} (smooth)").format(col_names[deaths]):
fit.smoothed_diff(data[deaths]),
},
index=data.index,
)
ax = smooth.plot(legend=False, lw=2, ax=ax)
# Prepare cases dataframe and plot it
kwargs.setdefault("alpha", 0.5)
new_cases = data.diff().fillna(0)
new_cases = new_cases.rename(col_names, axis=1)
if "ylim" not in kwargs:
deaths = new_cases.iloc[:, 1]
exp = np.log10(deaths[deaths > 0]).mean()
exp = min(10, int(exp / 2))
kwargs["ylim"] = (10**exp, None)
ax: plt.Axes = new_cases.plot.bar(width=1.0, ax=ax, **kwargs)
# Fix xticks
periods = 7 if dates else 10
xticks = ax.get_xticks()
labels = ax.get_xticklabels()
ax.set_xticks(xticks[::periods])
ax.set_xticklabels(labels[::periods])
ax.tick_params("x", rotation=0)
ax.set_ylim(1, None)
if tight_layout:
fig = ax.get_figure()
fig.tight_layout()
return ax
def plot_map(self,
im: np.array,
title: str = '',
cbar_unit: str = None,
tag: str = None,
meta: dict = None,
cmap: str = 'viridis',
view_extent: np.array = None,
outline: bool = False,
points: bool = False,
point_color: bool = False,
rectangle: bool = False,
labels: bool = False,
ticks: bool = True,
scamap: bool = None,
ax: plt.Axes = None,
hillshade: bool = False,
scale_dict: dict = None,
grid: bool = True,
alpha: float = 1,
showplot: bool = False,
sci: bool = False,
figsize: tuple = None,
ashape: bool = None):
# Main plotting function. Ensures that all other plots have the same parameters
""" Inputs:
im: The 3D np array to be plotted. Can be the DEM, the thickness, the error, etc.
title: The title of the plot
cbar_unit: The units of the color bar
tag: The tag of the plot with which it will be saved
cmap: The colormap wanted for the plot, defaults to viridis
view_extent: The extent wanted for the plot. Defaults to None which will set the extent to the whole map.
Takes as input a numpy array, like the self.point_extent array
Outline: Boolean value, defaults to False. Set to true if you want the outline plotted on the map.
points: Boolean value, defaults to False. Set to true if you want the points plotted on the map.
point_color: Boolean value, defaults to False. Set to true if you want the points colored by the thickness.
Could be changed in the future to a scalar map instead of a boolean.
rectangle: Boolean value, defaults to False. Set to true if you want a rectangle outlining the points' extent
in the map. CURRENTLY DOESN'T WORK PROPERLY
labels: Boolean value, defaults to False. Set to true if you want the x and y labels plotted.
ticks: Boolean value, defaults to True. Set to true if you want the x and y ticks plotted.
scamap: Scalarmap object, defaults to None. Set if you want a specific colormap scale. Useful for subplots.
ax: matplotlib Ax object, defaults to None. Set if you want to specify on which ax to plot.
Useful for subplots.
hillshade: Boolean value, defaults to False. Set for a hillshade effect, especially on DEMs
scale: Dictionary, defaults to None. Parameters to add a scale to the map
alpha: Float defaults to 1. Sets the transparency of the main map image
showplot: Boolean, defaults to False. Set to true if you want to see the figure. Only pops up if
no ax object is provided.
"""
# Gets the two last dimensions of the 3D array. Needed because rasters from rasterio are of (1, m, n) size
if len(im.shape) == 3:
im = im[0]
if meta is None:
meta = self.meta
# Manages the extent array. The order needed here is different than given from the shapely format
b = [0, 2, 1, 3]
extent = [
rasterio.transform.array_bounds(*im.shape, meta['transform'])[i]
for i in b
]
xmin, xmax, ymin, ymax = [self.outline.total_bounds[i] for i in b]
if view_extent is not None:
view_extent = [view_extent[i] for i in b]
xmin, xmax, ymin, ymax = view_extent
fig = None
if ax is None:
fig = plt.figure(figsize=figsize, tight_layout=True)
ax = plt.gca()
# Plot the image and add a colorbar
if scamap is None:
norm = Normalize(np.nanmin(im), np.nanmax(im))
scamap = plt.cm.ScalarMappable(cmap=cmap, norm=norm)
if hillshade:
hills = im_to_hillshade(self.dem_im[0], 225, 40)
ax.imshow(hills, extent=[self.extent[i] for i in b], cmap='Greys')
img = ax.imshow(im, cmap=cmap, extent=extent, alpha=alpha)
if cbar_unit is not None:
divider = make_axes_locatable(ax)
cax = divider.append_axes('right', size=0.2, pad=0.1)
cbar = plt.colorbar(img, cax=cax, orientation='vertical')
cbar.ax.get_yaxis().labelpad = 15
cbar.ax.set_title(f'{cbar_unit}')
c = 'black'
e = None
if point_color:
c = scamap.to_rgba(self.gpr.iloc[:, 2])
e = 'black'
# Plots various map accessories if asked
if points:
lw = 0.1
if len(self.gpr) > 1000:
lw = 0
ax.scatter(self.gpr.geometry.x,
self.gpr.geometry.y,
c=c,
cmap=cmap,
edgecolors=e,
linewidths=lw)
if outline:
self.outline.plot(ax=ax, facecolor='None', edgecolor='black')
if rectangle:
rec = self.create_rectangle(color='red', lw=1)
ax.add_patch(rec)
if ashape:
x, y = self.ashape.unary_union.exterior.xy
ax.plot(x, y, color='red', lw=1)
if scale_dict is not None:
scale_dict = parse_scale_dict(scale_dict)
y_offset = (ymax - ymin) * scale_dict['y_offset']
x_offset = (xmax - xmin) * scale_dict['x_offset']
length = scale_dict['length']
label_length = length
if scale_dict['units'] == 'km':
length *= 1000
xs = [xmin + x_offset, xmin + x_offset + length]
ys = [ymin + y_offset, ymin + y_offset]
bar = ax.plot(xs, ys, linewidth=5, color=scale_dict['color'])
txt = ax.text(np.mean(xs),
np.mean(ys) + y_offset *
(1 + 0.05 / scale_dict['y_offset']),
f'{label_length} {scale_dict["units"]}',
ha='center',
va='center',
color=scale_dict['color'])
# txt.set_path_effects([pe.withStroke(linewidth=5, foreground='w')])
# Customises the map
ax.set_title(f'{title}')
ax.set_xlim(xmin, xmax)
ax.set_ylim(ymin, ymax)
ax.set_aspect('equal')
if labels:
ax.set_xlabel('Eastings [m]')
ax.set_ylabel('Northing [m]')
if ticks:
if sci:
ax.ticklabel_format(axis='both', style='sci', scilimits=(0, 0))
else:
ax.set_yticklabels(
['{:,.0f}'.format(y) for y in ax.get_yticks().tolist()])
ax.set_xticklabels(
['{:,.0f}'.format(x) for x in ax.get_xticks().tolist()],
rotation=-45)
else:
ax.set_yticklabels([])
ax.set_xticklabels([])
ax.set_xticks([])
ax.set_yticks([])
if grid:
ax.grid()
# Defines a custom legend for the outline due to a geopandas bug
# Currently no legend, need to figure out something for every model and dem source
"""handles, labels = ax.get_legend_handles_labels()
handles.append(mlines.Line2D([], [], color='black', label=data['outline']))
handles.append(matplotlib.patches.Patch (color='none', label=crs))
ax.legend(handles=handles, bbox_to_anchor=(0.5, data['leg_pos']), loc="lower center",
bbox_transform=fig.transFigure, ncol=len(handles), frameon=True)"""
if fig is not None:
if showplot:
plt.show()
if tag is not None:
fig.savefig(f'{self.img_folder}/{tag}.png',
bbox_inches='tight')
return fig, ax
else:
return img