Allow specifying file format for visualization (#85)

So far, it was only possible to generate PNGs. This is still the default, but can be changed to any other format supported by matplotlib

Author: dweindl

petab/visualize/plot_data_and_simulation.py

@@ -372,7 +372,9 @@ def plot_with_vis_spec(
         measurements_df: Optional[Union[str, pd.DataFrame]] = None,
         simulations_df: Optional[Union[str, pd.DataFrame]] = None,
         subplot_dir: Optional[str] = None,
-        plotter_type: str = 'mpl') -> Optional[Dict[str, plt.Subplot]]:
+        plotter_type: str = 'mpl',
+        format_: str = 'png',
+) -> Optional[Dict[str, plt.Subplot]]:
     """
     Plot measurements and/or simulations. Specification of the visualization
     routines is provided in visualization table.
@@ -394,6 +396,9 @@ def plot_with_vis_spec(
     plotter_type:
         Specifies which library should be used for plot generation. Currently,
         only matplotlib is supported.
+    format_:
+        File format for the generated figure.
+        (See :py:func:`matplotlib.pyplot.savefig` for supported options).
 
     Returns
     -------
@@ -415,8 +420,8 @@ def plot_with_vis_spec(
     else:
         raise NotImplementedError('Currently, only visualization with '
                                   'matplotlib is possible.')
-    ax = plotter.generate_figure(subplot_dir)
-    return ax
+
+    return plotter.generate_figure(subplot_dir, format_=format_)
 
 
 def plot_without_vis_spec(
@@ -427,7 +432,8 @@ def plot_without_vis_spec(
         simulations_df: Optional[Union[str, pd.DataFrame]] = None,
         plotted_noise: str = MEAN_AND_SD,
         subplot_dir: Optional[str] = None,
-        plotter_type: str = 'mpl'
+        plotter_type: str = 'mpl',
+        format_: str = 'png',
 ) -> Optional[Dict[str, plt.Subplot]]:
     """
     Plot measurements and/or simulations. What exactly should be plotted is
@@ -462,6 +468,9 @@ def plot_without_vis_spec(
     plotter_type:
         Specifies which library should be used for plot generation. Currently,
         only matplotlib is supported
+    format_:
+        File format for the generated figure.
+        (See :py:func:`matplotlib.pyplot.savefig` for supported options).
 
     Returns
     -------
@@ -484,8 +493,8 @@ def plot_without_vis_spec(
     else:
         raise NotImplementedError('Currently, only visualization with '
                                   'matplotlib is possible.')
-    ax = plotter.generate_figure(subplot_dir)
-    return ax
+
+    return plotter.generate_figure(subplot_dir, format_=format_)
 
 
 def plot_problem(petab_problem: problem.Problem,

petab/visualize/plotter.py

@@ -321,8 +321,11 @@ def ticks(y, _):
         ax.set_ylabel(
             subplot.yLabel)
 
-    def generate_figure(self, subplot_dir: Optional[str] = None
-                        ) -> Optional[Dict[str, plt.Subplot]]:
+    def generate_figure(
+            self,
+            subplot_dir: Optional[str] = None,
+            format_: str = 'png',
+    ) -> Optional[Dict[str, plt.Subplot]]:
         """
         Generate the full figure based on the markup in the figure attribute.
 
@@ -331,6 +334,9 @@ def generate_figure(self, subplot_dir: Optional[str] = None
         subplot_dir:
             A path to the folder where single subplots should be saved.
             PlotIDs will be taken as file names.
+        format_:
+            File format for the generated figure.
+            (See :py:func:`matplotlib.pyplot.savefig` for supported options).
 
         Returns
         -------
@@ -378,7 +384,7 @@ def generate_figure(self, subplot_dir: Optional[str] = None
                 # TODO: why this doesn't work?
                 plt.tight_layout()
                 plt.savefig(os.path.join(subplot_dir,
-                                         f'{subplot.plotId}.png'))
+                                         f'{subplot.plotId}.{format_}'))
                 plt.close()
 
         if subplot_dir is None: