Add title to pyplot window

When using pyplot to plot the results, the window
name is based on the dataset title and the view
title.

src/msspec/iodata.py

@@ -17,7 +17,7 @@
 # along with this msspec.  If not, see <http://www.gnu.org/licenses/>.
 #
 # Source file  : src/msspec/iodata.py
-# Last modified: Mon, 16 Jun 2025 14:42:03 +0200
+# Last modified: Wed, 18 Jun 2025 11:46:41 +0200
 # Committed by : Sylvain Tricot <sylvain.tricot@univ-rennes.fr>
 
 
@@ -84,6 +84,7 @@ from lxml import etree
 from matplotlib.backends.backend_agg import FigureCanvasAgg
 #from matplotlib.backends.backend_cairo import FigureCanvasCairo as FigureCanvasAgg
 from matplotlib.figure import Figure
+from matplotlib import pyplot as plt
 from terminaltables import AsciiTable
 
 import msspec
@@ -336,6 +337,15 @@ class DataSet(object):
         except:
             pass
 
+    def get_views(self):
+        """Returns all the defined views in the dataset.
+
+        :return: A list of view
+        :rtype: List of :py:class:`iodata._DataSetView`
+        """
+        return self._views
+
+    @property
     def views(self):
         """Returns all the defined views in the dataset.
 
@@ -365,6 +375,12 @@ class DataSet(object):
             mydset.add_parameter(name='Spectrometer', group='misc', value='Omicron', unit='')
 
         """
+        group = kwargs.get('group')
+        name = kwargs.get('name')
+        r = self.get_parameter(group=group, name=name)
+        if r:
+            r.update(**kwargs)
+        else:
             self._parameters.append(kwargs)
 
     def parameters(self):
@@ -398,12 +414,19 @@ class DataSet(object):
                     p.append(_)
         return p[0] if len(p) == 1 else p
 
+    def set_cluster(self, cluster):
+        clusbuf = StringIO()
+        cluster.info['absorber'] = cluster.absorber
+        write_xyz(clusbuf, cluster)
+        self.add_parameter(group='Cluster', name='cluster', value=clusbuf.getvalue(), hidden="True")
+
     def get_cluster(self):
         """Get all the atoms in the cluster.
 
         :return: The cluster
         :rtype: :py:class:`ase.Atoms`
         """
+        try:
             p = self.get_parameter(group='Cluster', name='cluster')['value']
             s = StringIO()
             s.write(self.get_parameter(group='Cluster', name='cluster')['value'])
@@ -411,17 +434,19 @@ class DataSet(object):
             #return ase.io.read(s, format='xyz')
             cluster = list(read_xyz(s))[-1]
             return cluster
+        except:
+            return None
 
 
     def select(self, *args, **kwargs):
         condition = kwargs.get('where', 'True')
         indices = []
 
-    def export_views(self, folder):
+    def export_views(self, folder, dpi=100):
-        for view in self.views():
+        for view in self.get_views():
             f = view.get_figure()
             fname = os.path.join(folder, view.title) + '.png'
-            f.savefig(fname)
+            f.savefig(fname, dpi=dpi)
 
 
     def export(self, filename="", mode="w"):
@@ -671,6 +696,7 @@ class Data(object):
                     return
             else:
                 data_grp = fd.create_group('DATA')
+                data_grp.attrs['dset_names'] = titles
                 meta_grp = fd.create_group('MsSpec viewer metainfo')
 
             data_grp.attrs['title'] = self.title
@@ -681,6 +707,7 @@ class Data(object):
                     continue
                 grp = data_grp.create_group(dset.title)
                 grp.attrs['notes'] = dset.notes
+                grp.attrs['col_names'] = dset.columns()
                 for col_name in dset.columns():
                     data = dset[col_name]
                     grp.create_dataset(col_name, data=data)
@@ -691,7 +718,7 @@ class Data(object):
             # xmlize views
             for dset in self._datasets:
                 views_node = etree.SubElement(root, 'views', dataset=dset.title)
-                for view in dset.views():
+                for view in dset.get_views():
                     view_el = etree.fromstring(view.to_xml())
                     views_node.append(view_el)
 
@@ -712,7 +739,7 @@ class Data(object):
         self._dirty = False
         LOGGER.info('Data saved in {}'.format(os.path.abspath(filename)))
 
-    def export(self, folder, overwrite=False):
+    def export(self, folder, overwrite=False, dpi=150):
         os.makedirs(folder, exist_ok=overwrite)
         for dset in self._datasets:
             dset_name = dset.title.replace(' ', '_')
@@ -720,7 +747,7 @@ class Data(object):
             os.makedirs(p, exist_ok=overwrite)
             fname = os.path.join(p, dset_name) + '.txt'
             dset.export(fname)
-            dset.export_views(p)
+            dset.export_views(p, dpi=dpi)
 
     @staticmethod
     def load(filename):
@@ -737,12 +764,20 @@ class Data(object):
             views = {}
 
             output.title = fd['DATA'].attrs['title']
-            for dset_name in fd['DATA'] :
+            try:
+                dset_names = fd['DATA'].attrs['dset_names']
+            except:
+                dset_names = [_ for _ in fd['DATA']]
+            for dset_name in dset_names:
                 parameters[dset_name] = []
                 views[dset_name] = []
                 dset = output.add_dset(dset_name)
                 dset.notes = fd['DATA'][dset_name].attrs['notes']
-                for h5dset in fd['DATA'][dset_name]:
+                try:
+                    col_names = fd['DATA'][dset_name].attrs['col_names']
+                except:
+                    col_names = [_ for _ in fd['DATA'][dset_name]]
+                for h5dset in col_names:
                     dset.add_columns(**{h5dset: fd['DATA'][dset_name][h5dset][...]})
 
             try:
@@ -870,10 +905,19 @@ class _DataSetView(object):
             data.append(values)
         return data
 
-    def get_figure(self):
+    def plot(self):
+        f = self.get_figure(backend='plt')
+        return f, f.get_axes()[0]
+
+
+    def get_figure(self, backend=None):
         opts = self._plotopts
 
-        figure = Figure(figsize=(3,2))
+        if backend is None:
+            figure = Figure()
+        else:
+            figure = plt.figure(num="[{}][{}]".format(self.dataset.title, self.title))
+
         axes = None
         proj = opts['projection']
         scale = opts['scale']
@@ -1113,7 +1157,7 @@ if has_gui:
                 self.notebooks[dset.title] = nb
                 #self.GetSizer().Add(nb, 1, wx.ALL|wx.EXPAND)
                 self.GetSizer().Add(nb, proportion=1, flag=wx.ALL|wx.EXPAND)
-                for view in dset.views():
+                for view in dset.get_views():
                     self.create_page(nb, view)
 
             self.create_menu()
@@ -1291,6 +1335,10 @@ if has_gui:
             self.Layout()
             self.update_statusbar()
             self._current_dset = name
+            has_cluster = True if self.data[self._current_dset].get_cluster() is not None else False
+            menu_item = self.GetMenuBar().FindItemById(302)
+            menu_item.Enable(has_cluster)
+
 
         def create_page(self, nb, view):
             # Get the matplotlib figure
@@ -1324,95 +1372,6 @@ if has_gui:
             nb.AddPage(p, view.title)
             canvas.draw()
 
-
-        def OLDcreate_page(self, nb, view):
-            opts = view._plotopts
-            p = wx.Panel(nb, -1)
-
-            figure = Figure()
-
-            axes = None
-            proj = opts['projection']
-            scale = opts['scale']
-            if proj == 'rectilinear':
-                axes = figure.add_subplot(111, projection='rectilinear')
-            elif proj in ('polar', 'ortho', 'stereo'):
-                axes = figure.add_subplot(111, projection='polar')
-
-            canvas = FigureCanvas(p, -1, figure)
-            sizer = wx.BoxSizer(wx.VERTICAL)
-
-            toolbar = NavigationToolbar2WxAgg(canvas)
-            toolbar.Realize()
-
-            sizer.Add(toolbar, 0, wx.ALL|wx.EXPAND)
-            toolbar.update()
-
-            sizer.Add(canvas, 5, wx.ALL|wx.EXPAND)
-
-            p.SetSizer(sizer)
-            p.Fit()
-            p.Show()
-
-
-            for values, label in zip(view.get_data(), opts['legend']):
-                # if we have only one column to plot, select a bar graph
-                if np.shape(values)[0] == 1:
-                    xvalues = list(range(len(values[0])))
-                    axes.bar(xvalues, values[0], label=label,
-                            picker=5)
-                    axes.set_xticks(xvalues)
-                else:
-                    if proj in ('ortho', 'stereo'):
-                        theta, phi, Xsec = cols2matrix(*values)
-                        theta_ticks = np.arange(0, 91, 15)
-                        if proj == 'ortho':
-                            R = np.sin(np.radians(theta))
-                            R_ticks = np.sin(np.radians(theta_ticks))
-                        elif proj == 'stereo':
-                            R = 2 * np.tan(np.radians(theta/2.))
-                            R_ticks = 2 * np.tan(np.radians(theta_ticks/2.))
-                        #R = np.tan(np.radians(theta/2.))
-                        X, Y = np.meshgrid(np.radians(phi), R)
-                        im = axes.pcolormesh(X, Y, Xsec)
-                        axes.set_yticks(R_ticks)
-                        axes.set_yticklabels(theta_ticks)
-
-                        figure.colorbar(im)
-
-                    elif proj == 'polar':
-                        values[0] = np.radians(values[0])
-                        axes.plot(*values, label=label, picker=5,
-                                marker=opts['marker'])
-                    else:
-                        if scale == 'semilogx':
-                            pltcmd = axes.semilogx
-                        elif scale == 'semilogy':
-                            pltcmd = axes.semilogy
-                        elif scale == 'log':
-                            pltcmd = axes.loglog
-                        else:
-                            pltcmd = axes.plot
-                        pltcmd(*values, label=label, picker=5,
-                            marker=opts['marker'])
-                axes.grid(opts['grid'])
-                axes.set_title(opts['title'])
-                axes.set_xlabel(opts['xlabel'])
-                axes.set_ylabel(opts['ylabel'])
-                axes.set_xlim(*opts['xlim'])
-                axes.set_ylim(*opts['ylim'])
-                if label:
-                    axes.legend()
-            axes.autoscale(enable=opts['autoscale'])
-
-
-            # MPL events
-            figure.canvas.mpl_connect('motion_notify_event', self.on_mpl_motion)
-            figure.canvas.mpl_connect('pick_event', self.on_mpl_pick)
-
-            nb.AddPage(p, view.title)
-
-
         def update_statusbar(self):
             sb = self.GetStatusBar()
             menu_id = self.GetMenuBar().FindMenu('Datasets')