Fixes plot bug when resample is set on a subset of contrast

StephenNneji · Oct 16, 2025 · Oct 14, 2025 · Oct 15, 2025 · Oct 15, 2025 · Oct 14, 2025
commit e73b35a8c32d8cb52772d29e30f6b4ae0680da5c
diff --git a/pyproject.toml b/pyproject.toml
@@ -22,6 +22,10 @@ dependencies = [
     "tqdm>=4.66.5",
 ]
 
+[project.urls]
+Documentation = "https://rascalsoftware.github.io/RAT/"
+Repository = "https://github.com/RascalSoftware/python-RAT"
+
 [project.optional-dependencies]
 dev = [
     "pytest>=7.4.0",

diff --git a/ratapi/utils/plotting.py b/ratapi/utils/plotting.py
@@ -76,9 +76,9 @@ def _extract_plot_data(event_data: PlotEventData, q4: bool, show_error_bar: bool
         for j in range(len(sld)):
             results["sld"][-1].append([sld[j][:, 0], sld[j][:, 1]])
 
+        results["sld_resample"].append([])
         if event_data.resample[i] == 1 or event_data.modelType == "custom xy":
             layers = event_data.resampledLayers[i][0]
-            results["sld_resample"].append([])
             for j in range(len(event_data.resampledLayers[i])):
                 layer = event_data.resampledLayers[i][j]
                 if layers.shape[1] == 4:
@@ -198,7 +198,7 @@ def plot_ref_sld_helper(
                 sld_min, sld_max = confidence_intervals["sld"][i][j]
                 sld_plot.fill_between(plot_data["sld"][i][j][0], sld_min, sld_max, alpha=0.6, color="grey")
 
-        if plot_data["sld_resample"]:
+        if plot_data["sld_resample"] and plot_data["sld_resample"][i]:
             for j in range(len(plot_data["sld_resample"][i])):
                 sld_plot.plot(
                     plot_data["sld_resample"][i][j][0],
@@ -544,7 +544,7 @@ def update_foreground(self, data):
                 self.figure.axes[1].draw_artist(self.figure.axes[1].lines[i])
                 i += 1
 
-            if plot_data["sld_resample"]:
+            if plot_data["sld_resample"] and plot_data["sld_resample"][j]:
                 for resampled in plot_data["sld_resample"][j]:
                     self.figure.axes[1].lines[i].set_data(resampled[0], resampled[1])
                     self.figure.axes[1].draw_artist(self.figure.axes[1].lines[i])
@@ -982,10 +982,7 @@ def plot_contour(
 
 
 def panel_plot_helper(
-    plot_func: Callable,
-    indices: list[int],
-    fig: matplotlib.figure.Figure | None = None,
-    progress_callback: Callable[[int, int], None] | None = None,
+    plot_func: Callable, indices: list[int], fig: matplotlib.figure.Figure | None = None
 ) -> matplotlib.figure.Figure:
     """Generate a panel-based plot from a single plot function.
 
@@ -997,9 +994,6 @@ def panel_plot_helper(
         The list of indices to pass into ``plot_func``.
     fig : matplotlib.figure.Figure, optional
         The figure object to use for plot.
-    progress_callback: Union[Callable[[int, int], None], None]
-        Callback function for providing progress during plot creation
-        First argument is current completed sub plot and second is total number of sub plots
 
     Returns
     -------
@@ -1011,19 +1005,21 @@ def panel_plot_helper(
     nrows, ncols = ceil(sqrt(nplots)), round(sqrt(nplots))
 
     if fig is None:
-        fig = plt.subplots(nrows, ncols, figsize=(11, 10), subplot_kw={"visible": False})[0]
+        fig = plt.subplots(nrows, ncols, figsize=(11, 10))[0]
     else:
         fig.clf()
-        fig.subplots(nrows, ncols, subplot_kw={"visible": False})
+        fig.subplots(nrows, ncols)
     axs = fig.get_axes()
-    for index, plot_num in enumerate(indices):
-        axs[index].tick_params(which="both", labelsize="medium")
-        axs[index].xaxis.offsetText.set_fontsize("small")
-        axs[index].yaxis.offsetText.set_fontsize("small")
-        axs[index].set_visible(True)
-        plot_func(axs[index], plot_num)
-        if progress_callback is not None:
-            progress_callback(index, nplots)
+
+    for plot_num, index in enumerate(indices):
+        axs[plot_num].tick_params(which="both", labelsize="medium")
+        axs[plot_num].xaxis.offsetText.set_fontsize("small")
+        axs[plot_num].yaxis.offsetText.set_fontsize("small")
+        plot_func(axs[plot_num], index)
+
+    # blank unused plots
+    for i in range(nplots, len(axs)):
+        axs[i].set_visible(False)
 
     fig.tight_layout()
     return fig
@@ -1040,7 +1036,6 @@ def plot_hists(
     block: bool = False,
     fig: matplotlib.figure.Figure | None = None,
     return_fig: bool = False,
-    progress_callback: Callable[[int, int], None] | None = None,
     **hist_settings,
 ):
     """Plot marginalised posteriors for several parameters from a Bayesian analysis.
@@ -1077,9 +1072,6 @@ def plot_hists(
         The figure object to use for plot.
     return_fig: bool, default False
         If True, return the figure as an object instead of showing it.
-    progress_callback: Union[Callable[[int, int], None], None]
-        Callback function for providing progress during plot creation
-        First argument is current completed sub plot and second is total number of sub plots
     hist_settings :
         Settings passed to `np.histogram`. By default, the settings
         passed are `bins = 25` and `density = True`.
@@ -1138,7 +1130,6 @@ def validate_dens_type(dens_type: str | None, param: str):
         ),
         params,
         fig,
-        progress_callback,
     )
     if return_fig:
         return fig
@@ -1153,7 +1144,6 @@ def plot_chain(
     block: bool = False,
     fig: matplotlib.figure.Figure | None = None,
     return_fig: bool = False,
-    progress_callback: Callable[[int, int], None] | None = None,
 ):
     """Plot the MCMC chain for each parameter of a Bayesian analysis.
 
@@ -1172,9 +1162,6 @@ def plot_chain(
         The figure object to use for plot.
     return_fig: bool, default False
         If True, return the figure as an object instead of showing it.
-    progress_callback: Union[Callable[[int, int], None], None]
-        Callback function for providing progress during plot creation
-        First argument is current completed sub plot and second is total number of sub plots
 
     Returns
     -------
@@ -1200,7 +1187,7 @@ def plot_one_chain(axes: Axes, i: int):
         axes.plot(range(0, nsimulations, skip), chain[:, i][0:nsimulations:skip])
         axes.set_title(results.fitNames[i], fontsize="small")
 
-    fig = panel_plot_helper(plot_one_chain, params, fig, progress_callback)
+    fig = panel_plot_helper(plot_one_chain, params, fig=fig)
     if return_fig:
         return fig
     plt.show(block=block)

diff --git a/setup.py b/setup.py
@@ -151,12 +151,6 @@ def build_libraries(self, libraries):
 
 setup(
     name=PACKAGE_NAME,
-    author="",
-    author_email="",
-    url="https://github.com/RascalSoftware/python-RAT",
-    description="Python extension for the Reflectivity Analysis Toolbox (RAT)",
-    long_description=LONG_DESCRIPTION,
-    long_description_content_type="text/markdown",
     packages=find_packages(exclude=("tests",)),
     include_package_data=True,
     package_data={"": [get_shared_object_name(libevent[0])], "ratapi.examples": ["data/*.dat"]},