"""Module containing functionality to plot fitted traces."""
from __future__ import annotations
from typing import TYPE_CHECKING
from typing import Any
from warnings import warn
import matplotlib.pyplot as plt
from pyglotaran_extras.config.plot_config import use_plot_config
from pyglotaran_extras.deprecation import warn_deprecated
from pyglotaran_extras.io.utils import result_dataset_mapping
from pyglotaran_extras.plotting.style import PlotStyle
from pyglotaran_extras.plotting.utils import MinorSymLogLocator
from pyglotaran_extras.plotting.utils import PlotDuplicationWarning
from pyglotaran_extras.plotting.utils import add_cycler_if_not_none
from pyglotaran_extras.plotting.utils import add_unique_figure_legend
from pyglotaran_extras.plotting.utils import extract_dataset_scale
from pyglotaran_extras.plotting.utils import extract_irf_location
from pyglotaran_extras.plotting.utils import get_next_cycler_color
from pyglotaran_extras.plotting.utils import select_plot_wavelengths
from pyglotaran_extras.types import Unset
from pyglotaran_extras.types import UnsetType
__all__ = ["plot_fitted_traces", "select_plot_wavelengths"]
if TYPE_CHECKING:
from collections.abc import Iterable
import numpy as np
from cycler import Cycler
from matplotlib.axes import Axes
from matplotlib.figure import Figure
from pyglotaran_extras.types import ResultLike
[docs]
@use_plot_config(exclude_from_config=("cycler", "ax", "axis"))
def plot_data_and_fits(
result: ResultLike,
wavelength: float,
ax: Axes | UnsetType = Unset,
center_λ: float | None = None,
main_irf_nr: int = 0,
linlog: bool = False,
linthresh: float = 1,
divide_by_scale: bool = True,
per_axis_legend: bool = False,
y_label: str = "a.u.",
cycler: Cycler | None = PlotStyle().data_cycler_solid,
show_zero_line: bool = True,
axis: UnsetType = Unset,
) -> None:
"""Plot data and fits for a given ``wavelength`` on a given ``ax``.
If the wavelength isn't part of a dataset, that dataset will be skipped.
Parameters
----------
result : ResultLike
Data structure which can be converted to a mapping.
wavelength : float
Wavelength to plot data and fits for.
ax : Axes | UnsetType
Axes to plot the data and fits on. Defaults to Unset.
center_λ : float | None
Center wavelength (λ in nm)
main_irf_nr : int
Index of the main ``irf`` component when using an ``irf``
parametrized with multiple peaks. Defaults to 0.
linlog : bool
Whether to use 'symlog' scale or not. Defaults to False.
linthresh : float
A single float which defines the range (-x, x), within which the plot is linear.
This avoids having the plot go to infinity around zero. Defaults to 1.
divide_by_scale : bool
Whether or not to divide the data by the dataset scale used for optimization.
Defaults to True.
per_axis_legend : bool
Whether to use a legend per plot or for the whole figure. Defaults to False.
y_label : str
Label used for the y-axis of each subplot.
cycler : Cycler | None
Plot style cycler to use. Defaults to PlotStyle().data_cycler_solid.
show_zero_line : bool
Whether or not to add a horizontal line at zero. Defaults to True.
axis : UnsetType
Deprecated use ``ax`` instead. Defaults to Unset.
See Also
--------
plot_fit_overview
Raises
------
ValueError
If ``ax`` was not provided, ``ax`` should be a required argument but to facilitate the
deprecation ``axis`` -> ``ax`` it has a default of ``Unset``.
"""
if isinstance(ax, UnsetType) and not isinstance(axis, UnsetType):
warn_deprecated(
deprecated_qual_name_usage="axis",
new_qual_name_usage="ax",
to_be_removed_in_version="0.9.0",
)
ax = axis
if isinstance(ax, UnsetType):
msg = "Required argument ``ax`` wasn't set."
raise ValueError(msg)
result_map = result_dataset_mapping(result)
add_cycler_if_not_none(ax, cycler)
for dataset_name in result_map:
if result_map[dataset_name].coords["time"].to_numpy().size == 1:
continue
spectral_coords = result_map[dataset_name].coords["spectral"].to_numpy()
if spectral_coords.min() <= wavelength <= spectral_coords.max():
result_data = result_map[dataset_name].sel(spectral=[wavelength], method="nearest")
scale = extract_dataset_scale(result_data, divide_by_scale)
irf_loc = extract_irf_location(result_data, center_λ, main_irf_nr)
result_data = result_data.assign_coords(time=result_data.coords["time"] - irf_loc)
(result_data.data / scale).plot(x="time", ax=ax, label=f"{dataset_name}_data")
(result_data.fitted_data / scale).plot(x="time", ax=ax, label=f"{dataset_name}_fit")
else:
[get_next_cycler_color(ax) for _ in range(2)]
if linlog:
ax.set_xscale("symlog", linthresh=linthresh)
ax.xaxis.set_minor_locator(MinorSymLogLocator(linthresh))
if show_zero_line is True:
ax.axhline(0, color="k", linewidth=1)
ax.set_ylabel(y_label)
if per_axis_legend is True:
ax.legend()
[docs]
@use_plot_config(exclude_from_config=("cycler",))
def plot_fitted_traces(
result: ResultLike,
wavelengths: Iterable[float],
axes_shape: tuple[int, int] = (4, 4),
center_λ: float | None = None,
main_irf_nr: int = 0,
linlog: bool = False,
linthresh: float = 1,
divide_by_scale: bool = True,
per_axis_legend: bool = False,
figsize: tuple[float, float] = (30, 15),
title: str = "Fit overview",
y_label: str = "a.u.",
cycler: Cycler | None = PlotStyle().data_cycler_solid,
show_zero_line: bool = True,
) -> tuple[Figure, np.ndarray[Any, Axes]]:
"""Plot data and their fit in per wavelength plot grid.
Parameters
----------
result : ResultLike
Data structure which can be converted to a mapping of datasets.
wavelengths : Iterable[float]
Wavelength which should be used for each subplot, should to be of length N*M
with ``axes_shape`` being of shape (N, M), else it will result in missing plots.
axes_shape : tuple[int, int]
Shape of the plot grid (N, M). Defaults to (4, 4).
center_λ : float | None
Center wavelength of the IRF (λ in nm).
main_irf_nr : int
Index of the main ``irf`` component when using an ``irf``
parametrized with multiple peaks. Defaults to 0.
linlog : bool
Whether to use 'symlog' scale or not. Defaults to False.
linthresh : float
A single float which defines the range (-x, x), within which the plot is linear.
This avoids having the plot go to infinity around zero. Defaults to 1.
divide_by_scale : bool
Whether or not to divide the data by the dataset scale used for optimization.
Defaults to True.
per_axis_legend : bool
Whether to use a legend per plot or for the whole figure. Defaults to False.
figsize : tuple[float, float]
Size of the figure (N, M) in inches. Defaults to (30, 15).
title : str
Title to add to the figure. Defaults to "Fit overview".
y_label : str
Label used for the y-axis of each subplot.
cycler : Cycler | None
Plot style cycler to use. Defaults to PlotStyle().data_cycler_solid.
show_zero_line : bool
Whether or not to add a horizontal line at zero. Defaults to True.
Returns
-------
tuple[Figure, np.ndarray[Any, Axes]]
Figure and axes which can then be refined by the user.
See Also
--------
maximum_coordinate_range
add_unique_figure_legend
plot_data_and_fits
calculate_wavelengths
"""
result_map = result_dataset_mapping(result)
fig, axes = plt.subplots(*axes_shape, figsize=figsize)
nr_of_plots = len(axes.flatten())
max_spectral_values = max(
len(result_map[dataset_name].coords["spectral"]) for dataset_name in result_map
)
if nr_of_plots > max_spectral_values:
warn(
PlotDuplicationWarning(
f"The number of plots ({nr_of_plots}) exceeds the maximum number of "
f"spectral data points ({max_spectral_values}), "
"which will lead in duplicated plots."
),
stacklevel=2,
)
for wavelength, ax in zip(wavelengths, axes.flatten(), strict=True):
plot_data_and_fits(
result=result_map,
wavelength=wavelength,
ax=ax,
center_λ=center_λ,
main_irf_nr=main_irf_nr,
linlog=linlog,
linthresh=linthresh,
divide_by_scale=divide_by_scale,
per_axis_legend=per_axis_legend,
y_label=y_label,
cycler=cycler,
show_zero_line=show_zero_line,
)
if per_axis_legend is False:
add_unique_figure_legend(fig, axes)
fig.suptitle(title, fontsize=28)
fig.tight_layout()
return fig, axes
