✨ Add plot function for guidance spectra (#92)

* 👌 Prevent crash of plot_fitted_traces when guidance spectrum in result
* ✨ Added 'plot_guidance' function
* 👌 Fall back to plot_guidance in plot_overview for guidance spectrum instead of crashing
* 🩹 Respect figure_only argument for guidance case in plot_overview

pyglotaran_extras/__init__.py

@@ -2,6 +2,7 @@
 from pyglotaran_extras.io.load_data import load_data
 from pyglotaran_extras.io.setup_case_study import setup_case_study
 from pyglotaran_extras.plotting.plot_data import plot_data_overview
+from pyglotaran_extras.plotting.plot_guidance import plot_guidance
 from pyglotaran_extras.plotting.plot_overview import plot_overview
 from pyglotaran_extras.plotting.plot_overview import plot_simple_overview
 from pyglotaran_extras.plotting.plot_traces import plot_fitted_traces
@@ -15,6 +16,7 @@
     "plot_simple_overview",
     "plot_fitted_traces",
     "select_plot_wavelengths",
+    "plot_guidance",
 ]
 
 __version__ = "0.6.0"

pyglotaran_extras/plotting/plot_guidance.py

@@ -0,0 +1,65 @@
+"""Module containing guidance spectra plotting functionality."""
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
+import matplotlib.pyplot as plt
+
+from pyglotaran_extras.io.load_data import load_data
+from pyglotaran_extras.plotting.style import PlotStyle
+from pyglotaran_extras.plotting.utils import add_cycler_if_not_none
+
+if TYPE_CHECKING:
+    from cycler import Cycler
+    from matplotlib.figure import Figure
+    from matplotlib.pyplot import Axes
+
+    from pyglotaran_extras.types import DatasetConvertible
+
+
+def plot_guidance(
+    result: DatasetConvertible,
+    figsize: tuple[int, int] = (15, 5),
+    title: str = "Guidance Overview",
+    y_label: str = "a.u.",
+    cycler: Cycler | None = PlotStyle().cycler,
+) -> tuple[Figure, Axes]:
+    """Plot overview for a guidance spectrum.
+
+    Parameters
+    ----------
+    result: DatasetConvertible
+        Result from a pyglotaran optimization as dataset, Path or Result object.
+    figsize: tuple[int, int]
+        Size of the figure (N, M) in inches. Defaults to (15, 5)
+    title: str
+        Title to add to the figure. Defaults to "Guidance Overview"
+    y_label: str
+        Label used for the y-axis of each subplot. Defaults to "a.u."
+    cycler: Cycler | None
+        Plot style cycler to use. Defaults to PlotStyle().cycler.
+
+    Returns
+    -------
+    tuple[Figure, Axes]
+        Figure and axes which can then be refined by the user.
+    """
+    res = load_data(result)
+    fig, axes = plt.subplots(1, 2, figsize=figsize)
+
+    for axis in axes:
+        add_cycler_if_not_none(axis, cycler)
+
+    res.data.plot(x="spectral", ax=axes[0], label="data")
+    res.fitted_data.plot(x="spectral", ax=axes[0], label="fit")
+    res.residual.plot(x="spectral", ax=axes[1], label="residual")
+
+    for axis in axes:
+        axis.set_ylabel(y_label)
+    axes[0].legend()
+    axes[0].set_title("Fit quality")
+    axes[1].set_title("Residual")
+    fig.suptitle(title, fontsize=28)
+    plt.tight_layout()
+
+    return fig, axes

pyglotaran_extras/plotting/plot_overview.py

@@ -11,6 +11,7 @@
 from pyglotaran_extras.deprecation.deprecation_utils import PyglotaranExtrasApiDeprecationWarning
 from pyglotaran_extras.io.load_data import load_data
 from pyglotaran_extras.plotting.plot_concentrations import plot_concentrations
+from pyglotaran_extras.plotting.plot_guidance import plot_guidance
 from pyglotaran_extras.plotting.plot_residual import plot_residual
 from pyglotaran_extras.plotting.plot_spectra import plot_spectra
 from pyglotaran_extras.plotting.plot_svd import plot_svd
@@ -91,6 +92,12 @@ def plot_overview(
     """
     res = load_data(result)
 
+    if res.coords["time"].values.size == 1:
+        fig, axes = plot_guidance(res)
+        if figure_only is True:
+            return fig
+        return fig, axes
+
     # Plot dimensions
     M = 4
     N = 3
@@ -125,12 +132,10 @@ def plot_overview(
     plot_residual(
         res, axes[1, 0], linlog=linlog, linthresh=linthresh, show_data=show_data, cycler=cycler
     )
-    # plt.tight_layout(pad=3, w_pad=4.0, h_pad=4.0)
-    if figure_only is True:
-        warn(PyglotaranExtrasApiDeprecationWarning(FIG_ONLY_WARNING), stacklevel=2)
-        return fig
-    else:
+    if figure_only is False:
         return fig, axes
+    warn(PyglotaranExtrasApiDeprecationWarning(FIG_ONLY_WARNING), stacklevel=2)
+    return fig
 
 
 def plot_simple_overview(

pyglotaran_extras/plotting/plot_traces.py

@@ -80,6 +80,8 @@ def plot_data_and_fits(
     result_map = result_dataset_mapping(result)
     add_cycler_if_not_none(axis, cycler)
     for dataset_name in result_map.keys():
+        if result_map[dataset_name].coords["time"].values.size == 1:
+            continue
         spectral_coords = result_map[dataset_name].coords["spectral"].values
         if spectral_coords.min() <= wavelength <= spectral_coords.max():
             result_data = result_map[dataset_name].sel(spectral=[wavelength], method="nearest")
@@ -135,7 +137,7 @@ def plot_fitted_traces(
         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.
+        Defaults to True.
     per_axis_legend : bool
         Whether to use a legend per plot or for the whole figure. Defaults to False.
     figsize : tuple[int, int]