fix: address memory issues and corruption in fMRIPlot

At the same time, this PR ensures that all calls to ``plt.savefig()``
are followed by closing the figure.

Resolves: #129.
Closes: #130.

nireports/assembler/tests/test_report.py

@@ -87,6 +87,7 @@ def bids_sessions(tmpdir_factory):
         file_path = svg_dir / bids_path
         file_path.ensure()
         f.savefig(str(file_path))
+        f.clf()
 
     # create anatomical data
     anat_opts = [
@@ -110,6 +111,7 @@ def bids_sessions(tmpdir_factory):
         file_path = svg_dir / bids_path
         file_path.ensure()
         f.savefig(str(file_path))
+        f.clf()
 
     return svg_dir.dirname
 

nireports/interfaces/dmri.py

@@ -93,5 +93,7 @@ def _run_interface(self, runtime):
         )
 
         out_figure.savefig(self._results["out_file"], format="svg", dpi=300)
+        out_figure.clf()
+        out_figure = None
 
         return runtime

nireports/interfaces/fmri.py

@@ -98,7 +98,7 @@ def _run_interface(self, runtime):
             else nifti_timeseries(input_data, seg_file)
         )
 
-        fig = fMRIPlot(
+        fMRIPlot(
             dataset,
             segments=segments,
             spikes_files=(
@@ -109,6 +109,6 @@ def _run_interface(self, runtime):
             units={"outliers": "%", "FD": "mm"},
             vlines={"FD": [self.inputs.fd_thres]},
             nskip=self.inputs.drop_trs,
-        ).plot()
-        fig.savefig(self._results["out_file"], bbox_inches="tight")
+        ).plot(out_file=self._results["out_file"])
+
         return runtime

nireports/reportlets/modality/func.py

@@ -89,22 +89,25 @@ def __init__(
             for sp_file in spikes_files:
                 self.spikes.append((np.loadtxt(sp_file), None, False))
 
-    def plot(self, figure=None):
+    def plot(self, figure=None, out_file=None):
         """Main plotter"""
-        import seaborn as sns
-
-        sns.set_style("whitegrid")
-        sns.set_context("paper", font_scale=0.8)
 
         if figure is None:
-            figure = plt.gcf()
+            figure = plt.figure(figsize=(19.2, 32))
 
         nconfounds = len(self.confounds)
         nspikes = len(self.spikes)
         nrows = 1 + nconfounds + nspikes
 
         # Create grid
-        grid = GridSpec(nrows, 1, wspace=0.0, hspace=0.05, height_ratios=[1] * (nrows - 1) + [5])
+        grid = GridSpec(
+            nrows,
+            1,
+            figure=figure,
+            wspace=0.0,
+            hspace=0.05,
+            height_ratios=[1] * (nrows - 1) + [5],
+        )
 
         grid_id = 0
         for tsz, name, iszs in self.spikes:
@@ -130,4 +133,11 @@ def plot(self, figure=None):
             drop_trs=self.nskip,
             cmap="paired" if self.paired_carpet else None,
         )
+
+        if out_file is not None:
+            figure.savefig(out_file, bbox_inches="tight")
+            plt.close(figure)
+            figure = None
+            return out_file
+
         return figure

nireports/reportlets/nuisance.py

@@ -213,6 +213,7 @@ def plot_qi2(x_grid, ref_pdf, fit_pdf, ref_data, cutoff_idx, out_file=None):
         out_file = op.abspath("qi2_plot.svg")
 
     fig.savefig(out_file, bbox_inches="tight", pad_inches=0, dpi=300)
+    plt.close(fig=fig)
     return out_file
 
 
@@ -340,7 +341,6 @@ def plot_carpet(
         height_ratios=[len(v) for v in segments.values()],
     )
 
-    label = ""
     for i, (_, indices) in enumerate(segments.items()):
         # Carpet plot
         ax = plt.subplot(gs[i])
@@ -397,7 +397,7 @@ def plot_carpet(
             ax.set_title(title)
 
     if nsegments == 1:
-        ax.set_ylabel(label)
+        ax.set_ylabel(segments.keys()[0])
 
     if legend:
         from matplotlib.patches import Patch

nireports/reportlets/surface.py

@@ -158,7 +158,7 @@ def get_surface_meshes(density, surface_type):
 
     if output_file is not None:
         figure.savefig(output_file, bbox_inches="tight", dpi=400)
-        plt.close(figure)
+        figure.clf()
         return output_file
 
     return figure

nireports/reportlets/utils.py

@@ -153,6 +153,7 @@ def svg2str(display_object, dpi=300):
     display_object.frame_axes.figure.savefig(
         image_buf, dpi=dpi, format="svg", facecolor="k", edgecolor="k"
     )
+    display_object.frame_axes.figure.clf()
     image_buf.seek(0)
     return image_buf.getvalue()
 

nireports/reportlets/xca.py

@@ -367,9 +367,10 @@ def compcor_variance_plot(
             ax[m].spines[side].set_visible(False)
 
     if output_file is not None:
-        figure = plt.gcf()
-        figure.savefig(output_file, bbox_inches="tight")
-        plt.close(figure)
-        figure = None
+        if fig is None:
+            fig = plt.gcf()
+        fig.savefig(output_file, bbox_inches="tight")
+        fig.clf()
+        fig = None
         return output_file
     return ax

nireports/tests/test_dwi.py

@@ -58,6 +58,7 @@ def test_plot_dwi(tmp_path, testdata_path, outdir):
 
     if outdir is not None:
         plt.savefig(outdir / f"{stem}.svg", bbox_inches="tight")
+        plt.close(plt.gcf())
 
 
 @pytest.mark.parametrize(
@@ -77,6 +78,7 @@ def test_plot_gradients(tmp_path, testdata_path, dwi_btable, outdir):
 
     if outdir is not None:
         plt.savefig(outdir / f"{dwi_btable}.svg", bbox_inches="tight")
+        plt.close(plt.gcf())
 
 
 def test_plot_tissue_values(tmp_path):

nireports/tests/test_reportlets.py

@@ -173,6 +173,7 @@ def test_fmriplot(input_files, testdata_path, outdir):
             outdir / f"fmriplot_{dtype}{has_seg}.svg",
             bbox_inches="tight",
         )
+        fig.clf()
 
 
 def test_plot_melodic_components(tmp_path, outdir):