def save_figure(
fig_object: matplotlib.figure.Figure,
file_path: Text) -> None:
"""Fully saves the figure in pdf and pkl format for later modification.
This function saves the figure in a pkl and pdf such that later can
be loaded and easily be modified.
To have the figure object, one can add the following line of the code
to the beginning of their code:
fig_object = plt.figure()
Args:
fig_object: Figure object (computed by "plt.figure()")
file_path: Texting file path without file extension.
Returns:
None.
Raises:
None.
"""
# Saves as pdf.
fig_object.savefig(file_path + '.pdf', dpi=fig_object.dpi)
# Also saves as pickle.
with open(file_path + '.pkl', 'wb') as handle:
pk.dump(fig_object, handle, protocol=pk.HIGHEST_PROTOCOL)
def set_dim(
fig: matplotlib.figure.Figure,
width: float = 398.3386,
fraction_of_line_width: float = 1,
ratio: float = (5 ** 0.5 - 1) / 2,
) -> None:
"""Set aesthetic figure dimensions to avoid scaling in latex.
Default width is `src.constants.REPORT_WIDTH`.
Default ratio is golden ratio, with figure occupying full page width.
Args:
fig (matplotlib.figure.Figure): Figure object to resize.
width (float): Textwidth of the report to make fontsizes match.
Defaults to `src.constants.REPORT_WIDTH`.
fraction_of_line_width (float, optional): Fraction of the document width
which you wish the figure to occupy. Defaults to 1.
ratio (float, optional): Fraction of figure width that the figure height
should be. Defaults to (5 ** 0.5 - 1)/2.
Returns:
void; alters current figure to have the desired dimensions
Example:
Here is an example of using this function::
>>> set_dim(fig, fraction_of_line_width=1, ratio=(5 ** 0.5 - 1) / 2)
"""
fig.set_size_inches(
get_dim(width=width, fraction_of_line_width=fraction_of_line_width, ratio=ratio)
)
def update_figure(fig: mpl.figure.Figure,
params: Dict[str, str] = False) -> mpl.figure.Figure:
"""
Updates some mpl Figure parameters. Only limited support for now.
In a future version the optuna plots will be moved here
and expanded customization will be enabled.
Returns a matplotlib Figure
Inputs:
fig: a matplotlib Figure
params: a dictionary containing mpl fields
"""
if params is False:
fig.set_yscale("log")
mpl.rcParams.update({"figure.dpi": 300})
else:
if "rcparams" in params:
mpl.rcParams.update(**params["rcparams"])
if "set_xlim" in params:
fig.set_xlim(params["set_xlim"])
if "set_ylim" in params:
fig.set_ylim(params["set_ylim"])
if "set_xscale" in params:
fig.set_xscale(params["set_xscale"])
if "set_yscale" in params:
fig.set_yscale(params["set_yscale"])
plt.tight_layout()
return fig
def hfss_plot_convergences_report(convergence_t: pd.core.frame.DataFrame,
convergence_f: pd.core.frame.DataFrame,
fig: mpl.figure.Figure = None,
_display=True):
"""Plot convergence frequency vs. pass number if fig is None.
Plot delta frequency and solved elements vs. pass number.
Plot delta frequency vs. solved elements.
Args:
convergence_t (pandas.core.frame.DataFrame): Convergence vs pass number of the eigenemode freqs.
convergence_f (pandas.core.frame.DataFrame): Convergence vs pass number of the eigenemode freqs.
fig (matplotlib.figure.Figure, optional): A mpl figure. Defaults to None.
_display (bool, optional): Display the plot? Defaults to True.
"""
if fig is None:
fig = plt.figure(figsize=(11, 3.))
# Grid spec and axes; height_ratios=[4, 1], wspace=0.5
gs = mpl.gridspec.GridSpec(1, 3, width_ratios=[1.2, 1.5, 1])
axs = [fig.add_subplot(gs[i]) for i in range(3)]
ax0t = axs[1].twinx()
plot_convergence_f_vspass(axs[0], convergence_f)
plot_convergence_max_df(axs[1], convergence_t.iloc[:, 1])
plot_convergence_solved_elem(ax0t, convergence_t.iloc[:, 0])
plot_convergence_maxdf_vs_sol(axs[2], convergence_t.iloc[:, 1],
convergence_t.iloc[:, 0])
fig.tight_layout(w_pad=0.1) # pad=0.0, w_pad=0.1, h_pad=1.0)
def _save_fig(dst_path: str, figure: matplotlib.figure.Figure) -> None:
"""Save the generated figures for the dataset in dst_dir."""
# `savefig` do not support GCS, so first save the image locally.
with tempfile.TemporaryDirectory() as tmp_dir:
tmp_path = os.path.join(tmp_dir, 'tmp.png')
figure.savefig(tmp_path)
tf.io.gfile.copy(tmp_path, dst_path, overwrite=FLAGS.overwrite)
plt.close(figure)
def fig_to_image(fig: mpl.figure.Figure, **kwargs: dict) -> IO:
bbox_inches = kwargs.pop("bbox_inches", "tight")
format_ = "svg"
img = BytesIO()
fig.savefig(img, bbox_inches=bbox_inches, format=format_, **kwargs)
img.seek(0)
return img
def svg_from_mpl_axes(fig: mpl.figure.Figure) -> QByteArray:
""" Convert a matplotlib figure to SVG and store it in a Qt byte array.
"""
data = io.BytesIO()
fig.savefig(data, format="svg")
plt.close(fig)
return QByteArray(data.getvalue())
def fig_square(fig: mpl.figure.Figure) -> None:
"""Adjust figure width so that it is square, and tight layout.
Parameters
----------
fig : mpl.figure.Figure
`Figure` instance.
"""
fig.set_size_inches(mpl.figure.figaspect(1))
fig.tight_layout()
def save_figure(filename: Union[str, IO[bytes]],
fig: matplotlib.figure.Figure,
quality: Optional[int] = 90,
optimize: Optional[bool] = True) -> Tuple[int, int]:
"""Use Agg to save a figure to an image file and return dimensions."""
canvas = FigureCanvasAgg(fig)
canvas.draw()
_, _, width, height = canvas.figure.bbox.bounds
fig.savefig(filename, quality=quality, optimize=optimize)
return int(width), int(height)
def figure_to_base64str(fig: matplotlib.figure.Figure) -> str:
"""Converts a Matplotlib figure to a base64 string encoding.
Args:
fig: A matplotlib Figure.
Returns:
A base64 encoding of the figure.
"""
buf = io.BytesIO()
fig.savefig(buf, bbox_inches='tight', format='png')
return base64.b64encode(buf.getbuffer().tobytes()).decode('ascii')
def save_fig(fig: mpl.figure.Figure,
filename: str,
directory: Optional[str] = None,
add_date: bool = False,
**savefig_kwargs):
"""Saves a Matplotlib figure to disk."""
if add_date:
filename = "{}_{}".format(time.strftime("%Y%m%d"), filename)
savefig_kwargs.setdefault("bbox_inches", "tight")
savefig_kwargs.setdefault("pad_inches", 0.02)
save_path = os.path.join(directory, filename)
fig.savefig(save_path, **savefig_kwargs)
def multi_nyquist_title(fig: matplotlib.figure.Figure, params: paramsTup,
settings) -> matplotlib.figure.Figure:
# plt.figure(fig) # make sure fig is focus
(filename_strip, solv, elec, ref_elec, work_elec, voltage) = params
elec = "TBFTFB"
fig.suptitle(
f"Nyquist plots of {work_elec} in {elec} ({solv}) vs {ref_elec} reference",
y=0.98)
# xmin, xmax = plt.xlim() # pylint: disable=W0612
# expt_vars = f"WE = {work_elec} \nRE = {ref_elec} \nElectrolyte = {elec} \nSolvent = {solv}"
# fig.text(xmax * 1.1, 0, expt_vars, fontdict=settings, withdash=False)
return fig
def setsize(fig: matplotlib.figure.Figure) -> None:
"""
Set the size of a figure.
Currently the size is hardcoded, but functionality may be extended in the
future.
Arguments
---------
fig : matplotlib.figure.Figure
Figure to a be saved.
"""
fig.set_size_inches(11.75, 8.25) # a4
def subplot_data(fig: matplotlib.figure.Figure,
subplot_params: tuple,
timestamps: list,
data: np.array,
x_label: str,
y_label: str,
event_timestamps: list = None,
data_label: str = None,
fontsize: int = 30,
event_annotation_color='g') -> None:
'''Plots a given time series data on a subplot.
Keyword arguments:
fig -- matplotlib figure handle
subplot_params -- a tuple with three subplot parameters: number of rows,
number of columns, and the number of the current subplot
timestamps -- a list of timestamps (plotted over the x-axis)
data -- a one-dimensional numpy array of data items (plotted over the y-axis)
x_label -- x axis label
y_label -- y axis label
event_timestamps -- optional list of timestamps for data
annotation; the annotations are plotted as
lines at the given timestamps
(default None, in which case there are no annotations)
data_label -- optional label for the plotted data; if a label is given,
a legend is added to the plot (default None)
fontsize -- fontsize for the x and y axes labels (default 30)
event_annotation_color -- color of event annotation lines (default 'g')
'''
fig.add_subplot(*subplot_params)
# we plot the data
if data_label:
plt.plot(timestamps, data, label=data_label)
else:
plt.plot(timestamps, data)
# we add event annotations to the plot if there are any events
if event_timestamps is not None and len(event_timestamps) > 0:
plt.plot([event_timestamps, event_timestamps],
[np.nanmin(data), np.nanmax(data)],
event_annotation_color)
plt.xlabel(x_label, fontsize=fontsize)
plt.ylabel(y_label, fontsize=fontsize)
# we add a legend only if a data label is assigned
if data_label:
plt.legend()
def savefig(fig: matplotlib.figure.Figure, filename: str) -> None:
"""
Save a single figure to file.
Arguments
---------
fig : matplotlib.figure.Figure
Figure to a be saved.
filename : str
Name of the file to be written.
"""
print("saving figure {file}".format(file=filename))
matplotlib.pyplot.show(block=False)
fig.savefig(filename, dpi=300)
def style_figure(fig: matplotlib.figure.Figure, title: str, bottom: float = 0.2) -> None:
"""Stylize the supplied matplotlib Figure instance."""
fig.tight_layout()
if bottom is not None:
fig.subplots_adjust(bottom=bottom)
fig.suptitle(title)
fig.legend(ncol=10, handlelength=0.75, handletextpad=0.25, columnspacing=0.5, loc='lower left')
def _save_figure(fig: mpl.figure.Figure,
path: pathlib.Path,
close_figure: bool = False) -> None:
"""Saves a figure at a given location and optionally closes it.
Args:
fig (matplotlib.figure.Figure): figure to save
figure_path (pathlib.Path): path where figure should be saved
close_figure (bool, optional): whether to close figure after saving, defaults to
False
"""
path.parent.mkdir(parents=True, exist_ok=True)
log.debug(f"saving figure as {path}")
fig.savefig(path)
if close_figure:
plt.close(fig)
def add_parameter_details(f: matplotlib.figure.Figure, details: str, y: float):
if not details:
return
string = ""
elements = ["{} = {}".format(k, v) for k, v in json.loads(details).items()]
acc = 0
for el in elements[:-1]:
string = string + el + ','
acc += len(el) + 2
if acc > 60:
string = string + '\n'
acc = 0
else:
string = string + ' '
string += elements[-1]
f.text(0.05, y, string)
def _rdm_colorbar(
mappable: matplotlib.cm.ScalarMappable = None,
fig: matplotlib.figure.Figure = None,
ax: Axes = None,
title: str = None,
) -> matplotlib.colorbar.Colorbar:
"""_rdm_colorbar. Add vertically-oriented, small colorbar to rdm figure. Used
internally by show_rdm.
Args:
mappable (matplotlib.cm.ScalarMappable): Typically plt.imshow instance.
fig (matplotlib.figure.Figure): Matplotlib figure handle.
ax (matplotlib.axes._axes.Axes): Matplotlib axis handle. plt.gca() by default.
title (str): Title string for the colorbar (positioned top, left aligned).
Returns:
matplotlib.colorbar.Colorbar: Matplotlib handle.
"""
cb = fig.colorbar(
mappable=mappable,
ax=ax,
shrink=0.25,
aspect=5,
ticks=matplotlib.ticker.LinearLocator(numticks=3),
)
cb.ax.set_title(title, loc="left", fontdict=dict(fontweight="normal"))
return cb
def setup_ax(fig: matplotlib.figure.Figure,
pos: tuple[int, int, int] = (1, 1, 1),
) -> matplotlib.axes.Axes:
'''
Args
- fig: matplotlib.figure.Figure
- pos: 3-tuple of int, axes position (nrows, ncols, index)
Returns: matplotlib.axes.Axes
'''
ax = fig.add_subplot(*pos, projection=ccrs.PlateCarree())
# draw land (better version of cfeature.LAND)
# land = cfeature.NaturalEarthFeature(
# category='physical', name='land', scale='10m',
# edgecolor='face', facecolor=cfeature.COLORS['land'], zorder=-1)
ax.add_feature(cfeature.LAND)
# draw borders of countries (better version of cfeature.BORDERS)
countries = cfeature.NaturalEarthFeature(
category='cultural', name='admin_0_boundary_lines_land', scale='10m',
edgecolor='black', facecolor='none')
ax.add_feature(countries)
# draw coastline (better version of cfeature.COASTLINE)
coastline = cfeature.NaturalEarthFeature(
category='physical', name='coastline', scale='10m',
edgecolor='black', facecolor='none')
ax.add_feature(coastline)
# draw lakes (better version of cfeature.LAKES)
lakes = cfeature.NaturalEarthFeature(
category='physical', name='lakes', scale='10m',
edgecolor='face', facecolor=cfeature.COLORS['water'])
ax.add_feature(lakes)
# draw ocean (better version of cfeature.OCEAN)
ocean = cfeature.NaturalEarthFeature(
category='physical', name='ocean', scale='50m',
edgecolor='face', facecolor=cfeature.COLORS['water'], zorder=-1)
ax.add_feature(ocean)
# draw rivers (better version of cfeature.RIVERS)
rivers = cfeature.NaturalEarthFeature(
category='physical', name='rivers_lake_centerlines', scale='10m',
edgecolor=cfeature.COLORS['water'], facecolor='none')
ax.add_feature(rivers)
# draw borders of states/provinces internal to a country
states_provinces = cfeature.NaturalEarthFeature(
category='cultural', name='admin_1_states_provinces_lines', scale='50m',
edgecolor='gray', facecolor='none')
ax.add_feature(states_provinces)
ax.set_aspect('equal')
gridliner = ax.gridlines(draw_labels=True)
gridliner.top_labels = False
gridliner.right_labels = False
return ax
def add_metric_description_title(df_plot: pd.DataFrame,
fig: mpl.figure.Figure,
y: float = 1.0):
"""Adds a suptitle to the figure, describing the metric used."""
assert df_plot.Metric.nunique() == 1, "More than one metric in DataFrame."
binning_scheme = utils.assert_and_get_constant(df_plot.binning_scheme)
num_bins = utils.assert_and_get_constant(df_plot.num_bins)
norm = utils.assert_and_get_constant(df_plot.norm)
title = (f"ECE variant: {binning_scheme} binning, "
f"{num_bins:.0f} bins, "
f"{norm} norm")
display_names = {
"adaptive": "equal-mass",
"even": "equal-width",
"l1": "L1",
"l2": "L2",
}
for old, new in display_names.items():
title = title.replace(old, new)
fig.suptitle(title, y=y, verticalalignment="bottom")
def save_plot_impl(fig: matplotlib.figure.Figure,
output_prefix: str, output_name: str,
printing_extensions: Sequence[str]) -> List[str]:
""" Implementation of generic save plot function.
It loops over all requested file extensions and save the matplotlib fig.
Args:
fig: Figure on which the plot was drawn.
output_prefix: File path to where files should be saved.
output_name: Filename under which the plot should be saved, but without the file extension.
printing_extensions: List of file extensions under which plots should be saved. They should
not contain the dot!
Returns:
Filenames under which the plot was saved.
"""
filenames = []
for extension in printing_extensions:
filename = os.path.join(output_prefix, output_name + "." + extension)
logger.debug(f"Saving matplotlib figure to \"{filename}\"")
fig.savefig(filename)
filenames.append(filename)
return filenames
def plot_convergences(self,
convergence_t: pd.DataFrame = None,
convergence_f: pd.DataFrame = None,
fig: mpl.figure.Figure = None,
_display: bool = True):
"""Creates 3 plots, useful to determin the convergence achieved by the renderer:
* convergence frequency vs. pass number if fig is None.
* delta frequency and solved elements vs. pass number.
* delta frequency vs. solved elements.
Args:
convergence_t (pd.DataFrame): Convergence vs pass number of the eigenemode freqs.
convergence_f (pd.DataFrame): Convergence vs pass number of the eigenemode freqs.
fig (matplotlib.figure.Figure, optional): A mpl figure. Defaults to None.
_display (bool, optional): Display the plot? Defaults to True.
"""
if convergence_t is None:
convergence_t = self.convergence_t
if convergence_f is None:
convergence_f = self.convergence_f
if fig is None:
fig = plt.figure(figsize=(11, 3.))
# Grid spec and axes; height_ratios=[4, 1], wspace=0.5
gspec = mpl.gridspec.GridSpec(1, 3, width_ratios=[1.2, 1.5, 1])
axs = [fig.add_subplot(gspec[i]) for i in range(3)]
ax0t = axs[1].twinx()
plot_convergence_f_vspass(axs[0], convergence_f)
plot_convergence_max_df(axs[1], convergence_t.iloc[:, 1])
plot_convergence_solved_elem(ax0t, convergence_t.iloc[:, 0])
plot_convergence_maxdf_vs_sol(axs[2], convergence_t.iloc[:, 1],
convergence_t.iloc[:, 0])
fig.tight_layout(w_pad=0.1) # pad=0.0, w_pad=0.1, h_pad=1.0)
def add_stimulus(self, fig: matplotlib.figure.Figure, stim_path: Path):
"""
Add stimulus to a figure
Arguments:
fig {matplotlib.figure.Figure} -- [description]
Returns:
[type] -- [description]
"""
stim_path = Path(stim_path)
if stim_path.suffix == ".mp4":
vidcap = cv2.VideoCapture(str(stim_path))
success, image = vidcap.read()
else:
image = plt.imread(get_sample_data(stim_path))
newax = fig.add_axes([0.38, 0, 0.2, 0.4], zorder=-1)
newax.imshow(image)
newax.axis("off")
return fig
def apply(self, fig: matplotlib.figure.Figure) -> None:
# It shouldn't hurt to align the labels if there's only one.
fig.align_ylabels()
# Adjust the layout.
fig.tight_layout()
adjust_default_args = dict(
# Reduce spacing between subplots
hspace=0,
wspace=0,
# Reduce external spacing
left=0.10,
bottom=0.105,
right=0.98,
top=0.98,
)
adjust_default_args.update(self.edge_padding)
fig.subplots_adjust(**adjust_default_args)
def savefig(f: matplotlib.figure.Figure,
fpath: str,
tight: bool = True,
details: str = None,
space: float = 0.0,
**kwargs):
if tight:
if details:
add_parameter_details(f, details, -0.4 + space)
f.savefig(fpath, bbox_inches='tight', **kwargs)
else:
if details:
f.subplots_adjust(bottom=0.2)
add_parameter_details(f, details, 0.1)
f.savefig(fpath, **kwargs)
if fpath.endswith('png'):
add_tags_to_png_file(fpath)
if fpath.endswith('svg'):
add_tags_to_svg_file(fpath)
def _trends_helper(
adata: AnnData,
models: Dict[str, Dict[str, Any]],
gene: str,
ln_key: str,
lineage_names: Optional[Sequence[str]] = None,
same_plot: bool = False,
sharey: Union[str, bool] = False,
show_ylabel: bool = True,
show_lineage: bool = True,
show_xticks_and_label: bool = True,
lineage_cmap=None,
abs_prob_cmap=cm.viridis,
gene_as_title: bool = False,
legend_loc: Optional[str] = "best",
fig: mpl.figure.Figure = None,
axes: Union[mpl.axes.Axes, Sequence[mpl.axes.Axes]] = None,
**kwargs,
) -> None:
"""
Plot an expression gene for some lineages.
Parameters
----------
%(adata)s
%(model)s
gene
Name of the gene in `adata.var_names``.
ln_key
Key in ``adata.obsm`` where to find the lineages.
lineage_names
Names of lineages to plot.
same_plot
Whether to plot all lineages in the same plot or separately.
sharey
Whether the y-axis is being shared.
show_ylabel
Whether to show y-label on the y-axis. Usually, only the first column will contain the y-label.
show_lineage
Whether to show the lineage as the title. Usually, only first row will contain the lineage names.
show_xticks_and_label
Whether to show x-ticks and x-label. Usually, only the last row will show this.
lineage_cmap
Colormap to use when coloring the the lineage. If `None`, use colors from ``adata.uns``.
abs_prob_cmap:
Colormap to use when coloring in the absorption probabilities, if they are being plotted.
gene_as_title
Whether to use the gene names as titles (with lineage names as well) or on the y-axis.
legend_loc
Location of the legend. If `None`, don't show any legend.
fig
Figure to use.
ax
Ax to use.
**kwargs
Keyword arguments for :meth:`cellrank.ul.models.BaseModel.plot`.
Returns
-------
%(just_plots)s
"""
n_lineages = len(lineage_names)
if same_plot:
axes = [axes] * len(lineage_names)
fig.tight_layout()
axes = np.ravel(axes)
percs = kwargs.pop("perc", None)
if percs is None or not isinstance(percs[0], (tuple, list)):
percs = [percs]
same_perc = False # we need to show colorbar always if percs differ
if len(percs) != n_lineages or n_lineages == 1:
if len(percs) != 1:
raise ValueError(
f"Percentile must be a collection of size `1` or `{n_lineages}`, got `{len(percs)}`."
)
same_perc = True
percs = percs * n_lineages
hide_cells = kwargs.pop("hide_cells", False)
show_cbar = kwargs.pop("show_cbar", True)
if same_plot:
lineage_colors = (
lineage_cmap.colors
if lineage_cmap is not None and hasattr(lineage_cmap, "colors")
else adata.uns.get(f"{_colors(ln_key)}", cm.Set1.colors)
)
else:
lineage_colors = (
"black" if not mcolors.is_color_like(lineage_cmap) else lineage_cmap
)
for i, (name, ax, perc) in enumerate(zip(lineage_names, axes, percs)):
if same_plot:
if gene_as_title:
title = gene
ylabel = "expression" if show_ylabel else None
else:
title = ""
ylabel = gene
else:
if gene_as_title:
title = None
ylabel = "expression" if i == 0 else None
else:
title = (
(name if name is not None else "no lineage") if show_lineage else ""
)
ylabel = gene if i == 0 else None
models[gene][name].plot(
ax=ax,
fig=fig,
perc=perc,
show_cbar=False,
title=title,
hide_cells=hide_cells or (same_plot and i == n_lineages - 1),
same_plot=same_plot,
lineage_color=lineage_colors[i]
if same_plot and name is not None
else lineage_colors,
abs_prob_cmap=abs_prob_cmap,
ylabel=ylabel,
**kwargs,
)
if sharey in ("row", "all", True) and i == 0:
plt.setp(ax.get_yticklabels(), visible=True)
if show_xticks_and_label:
plt.setp(ax.get_xticklabels(), visible=True)
else:
ax.set_xlabel(None)
if not same_plot and same_perc and show_cbar and not hide_cells:
vmin = np.min([models[gene][ln].w_all for ln in lineage_names])
vmax = np.max([models[gene][ln].w_all for ln in lineage_names])
norm = mcolors.Normalize(vmin=vmin, vmax=vmax)
for ax in axes:
[
c
for c in ax.get_children()
if isinstance(c, mpl.collections.PathCollection)
][0].set_norm(norm)
divider = make_axes_locatable(ax)
cax = divider.append_axes("right", size="2.5%", pad=0.1)
_ = mpl.colorbar.ColorbarBase(
cax, norm=norm, cmap=abs_prob_cmap, label="absorption probability"
)
if same_plot and lineage_names != [None] and legend_loc is not None:
ax.legend(lineage_names, loc=legend_loc)
def plot_correlations(
fig: matplotlib.figure.Figure,
ax: matplotlib.axes.Axes,
r2: float,
slope: float,
y_inter: float,
corr_vals: np.ndarray,
vis_vals: np.ndarray,
scale_factor: Union[float, int],
corr_bname: str,
vis_bname: str,
odir: Union[Path, str],
):
"""
Plot the correlations between NIR band and the visible bands for
the Hedley et al. (2005) sunglint correction method
Parameters
----------
fig : matplotlib.figure object
Reusing a matplotlib.figure object to avoid the creation many
fig instantances
ax : matplotlib.axes._subplots object
Reusing the axes object
r2 : float
The correlation coefficient squared of the linear regression
between NIR and a VIS band
slope : float
The slope/gradient of the linear regression between NIR and
a VIS band
y_inter : float
The intercept of the linear regression between NIR and a
VIS band
corr_vals : numpy.ndarray
1D array containing the NIR values from the ROI
vis_vals : numpy.ndarray
1D array containing the VIS values from the ROI
scale_factor : int or None
The scale factor used to convert integers to reflectances
that range [0...1]
corr_bname : str
The NIR band number
vis_bname : str
The VIS band number
odir : str
Directory where the correlation plots are saved
"""
# clear previous plot
ax.clear()
# ----------------------------------- #
# Create a unique cmap for hist2d #
# ----------------------------------- #
ncolours = 256
# get the jet colormap
colour_array = plt.get_cmap("jet")(range(ncolours)) # 256 x 4
# change alpha values
# e.g. low values have alpha = 1, high values have alpha = 0
# color_array[:,-1] = np.linspace(1.0,0.0,ncolors)
# e.g. low values have alpha = 0, high values have alpha = 1
# color_array[:,-1] = np.linspace(0.0,1.0,ncolors)
# We want only the first few colours to have low alpha
# as they would represent low density [meshgrid] bins
# which we are not interested in, and hence would want
# them to appear as a white colour (alpha ~ 0)
num_alpha = 25
colour_array[0:num_alpha, -1] = np.linspace(0.0, 1.0, num_alpha)
colour_array[num_alpha:, -1] = 1
# create a colormap object
cmap = LinearSegmentedColormap.from_list(name="jet_alpha",
colors=colour_array)
# ----------------------------------- #
# Plot density using np.histogram2d #
# ----------------------------------- #
xbin_low, xbin_high = np.percentile(corr_vals, (1, 99),
interpolation="linear")
ybin_low, ybin_high = np.percentile(vis_vals, (1, 99),
interpolation="linear")
nbins = [int(xbin_high - xbin_low), int(ybin_high - ybin_low)]
bin_range = [[int(xbin_low), int(xbin_high)],
[int(ybin_low), int(ybin_high)]]
hist2d, xedges, yedges = np.histogram2d(x=corr_vals,
y=vis_vals,
bins=nbins,
range=bin_range)
# normalised hist to range [0...1] then rotate and flip
hist2d = np.flipud(np.rot90(hist2d / hist2d.max()))
# Mask zeros
hist_masked = np.ma.masked_where(hist2d == 0, hist2d)
# use pcolormesh to plot the hist2D
qm = ax.pcolormesh(xedges, yedges, hist_masked, cmap=cmap)
# create a colour bar axes within ax
cbaxes = inset_axes(
ax,
width="3%",
height="30%",
bbox_to_anchor=(0.37, 0.03, 1, 1),
loc="lower center",
bbox_transform=ax.transAxes,
)
# Add a colour bar inside the axes
fig.colorbar(
cm.ScalarMappable(cmap=cmap),
cax=cbaxes,
ticks=[0.0, 1],
orientation="vertical",
label="Point Density",
)
# ----------------------------------- #
# Plot linear regression line #
# ----------------------------------- #
x_range = np.array([xbin_low, xbin_high])
(ln, ) = ax.plot(
x_range,
slope * (x_range) + y_inter,
color="k",
linestyle="-",
label="linear regr.",
)
# ----------------------------------- #
# Format the figure #
# ----------------------------------- #
# add legend (top left)
lgnd = ax.legend(loc=2, fontsize=10)
# add annotation
ann_str = (r"$r^{2}$" + " = {0:0.2f}\n"
"slope = {1:0.2f}\n"
"y-inter = {2:0.2f}".format(r2, slope, y_inter))
ann = ax.annotate(ann_str,
xy=(0.02, 0.76),
xycoords="axes fraction",
fontsize=10)
# Add labels to figure
xlabel = f"Reflectance ({corr_bname})"
ylabel = f"Reflectance ({vis_bname})"
if scale_factor is not None:
if scale_factor > 1:
xlabel += " " + r"$\times$" + " {0}".format(int(scale_factor))
ylabel += " " + r"$\times$" + " {0}".format(int(scale_factor))
ax.set_xlabel(xlabel)
ax.set_ylabel(ylabel)
# plt.show(); sys.exit()
# Save figure
png_file = os.path.join(
odir, "Correlation_{0}_vs_{1}.png".format(corr_bname, vis_bname))
fig.savefig(png_file,
format="png",
bbox_inches="tight",
pad_inches=0.1,
dpi=300)
# delete all lines and annotations from figure,
# so it can be reused in the next iteration
qm.remove()
ln.remove()
ann.remove()
lgnd.remove()
def save(fig: matplotlib.figure.Figure, filename: str):
fig.savefig(filename)
def save_figure(fig: matplotlib.figure.Figure, name: str) -> None:
t_start = time()
print(f'Saving figure {name}...', end='')
fig.savefig(name)
print(f' ({time() - t_start:.2f} s)')
