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.
This commit is contained in:
Sylvain Tricot
parent
b15a5424d2
commit
c2e1384a5c
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@ -17,7 +17,7 @@
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# along with this msspec. If not, see <http://www.gnu.org/licenses/>.
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#
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# Source file : src/msspec/iodata.py
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# Last modified: Mon, 16 Jun 2025 14:42:03 +0200
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# Last modified: Wed, 18 Jun 2025 11:46:41 +0200
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# Committed by : Sylvain Tricot <sylvain.tricot@univ-rennes.fr>
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@ -84,6 +84,7 @@ from lxml import etree
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from matplotlib.backends.backend_agg import FigureCanvasAgg
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#from matplotlib.backends.backend_cairo import FigureCanvasCairo as FigureCanvasAgg
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from matplotlib.figure import Figure
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from matplotlib import pyplot as plt
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from terminaltables import AsciiTable
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import msspec
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@ -336,6 +337,15 @@ class DataSet(object):
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except:
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pass
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def get_views(self):
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"""Returns all the defined views in the dataset.
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:return: A list of view
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:rtype: List of :py:class:`iodata._DataSetView`
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"""
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return self._views
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@property
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def views(self):
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"""Returns all the defined views in the dataset.
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@ -365,7 +375,13 @@ class DataSet(object):
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mydset.add_parameter(name='Spectrometer', group='misc', value='Omicron', unit='')
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"""
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self._parameters.append(kwargs)
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group = kwargs.get('group')
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name = kwargs.get('name')
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r = self.get_parameter(group=group, name=name)
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if r:
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r.update(**kwargs)
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else:
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self._parameters.append(kwargs)
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def parameters(self):
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"""
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@ -398,30 +414,39 @@ class DataSet(object):
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p.append(_)
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return p[0] if len(p) == 1 else p
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def set_cluster(self, cluster):
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clusbuf = StringIO()
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cluster.info['absorber'] = cluster.absorber
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write_xyz(clusbuf, cluster)
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self.add_parameter(group='Cluster', name='cluster', value=clusbuf.getvalue(), hidden="True")
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def get_cluster(self):
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"""Get all the atoms in the cluster.
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:return: The cluster
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:rtype: :py:class:`ase.Atoms`
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"""
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p = self.get_parameter(group='Cluster', name='cluster')['value']
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s = StringIO()
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s.write(self.get_parameter(group='Cluster', name='cluster')['value'])
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s.seek(0)
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#return ase.io.read(s, format='xyz')
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cluster = list(read_xyz(s))[-1]
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return cluster
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try:
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p = self.get_parameter(group='Cluster', name='cluster')['value']
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s = StringIO()
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s.write(self.get_parameter(group='Cluster', name='cluster')['value'])
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s.seek(0)
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#return ase.io.read(s, format='xyz')
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cluster = list(read_xyz(s))[-1]
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return cluster
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except:
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return None
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def select(self, *args, **kwargs):
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condition = kwargs.get('where', 'True')
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indices = []
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def export_views(self, folder):
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for view in self.views():
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def export_views(self, folder, dpi=100):
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for view in self.get_views():
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f = view.get_figure()
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fname = os.path.join(folder, view.title) + '.png'
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f.savefig(fname)
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f.savefig(fname, dpi=dpi)
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def export(self, filename="", mode="w"):
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@ -671,6 +696,7 @@ class Data(object):
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return
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else:
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data_grp = fd.create_group('DATA')
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data_grp.attrs['dset_names'] = titles
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meta_grp = fd.create_group('MsSpec viewer metainfo')
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data_grp.attrs['title'] = self.title
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@ -681,6 +707,7 @@ class Data(object):
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continue
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grp = data_grp.create_group(dset.title)
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grp.attrs['notes'] = dset.notes
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grp.attrs['col_names'] = dset.columns()
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for col_name in dset.columns():
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data = dset[col_name]
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grp.create_dataset(col_name, data=data)
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@ -691,7 +718,7 @@ class Data(object):
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# xmlize views
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for dset in self._datasets:
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views_node = etree.SubElement(root, 'views', dataset=dset.title)
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for view in dset.views():
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for view in dset.get_views():
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view_el = etree.fromstring(view.to_xml())
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views_node.append(view_el)
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@ -712,7 +739,7 @@ class Data(object):
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self._dirty = False
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LOGGER.info('Data saved in {}'.format(os.path.abspath(filename)))
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def export(self, folder, overwrite=False):
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def export(self, folder, overwrite=False, dpi=150):
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os.makedirs(folder, exist_ok=overwrite)
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for dset in self._datasets:
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dset_name = dset.title.replace(' ', '_')
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@ -720,7 +747,7 @@ class Data(object):
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os.makedirs(p, exist_ok=overwrite)
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fname = os.path.join(p, dset_name) + '.txt'
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dset.export(fname)
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dset.export_views(p)
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dset.export_views(p, dpi=dpi)
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@staticmethod
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def load(filename):
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@ -737,12 +764,20 @@ class Data(object):
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views = {}
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output.title = fd['DATA'].attrs['title']
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for dset_name in fd['DATA'] :
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try:
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dset_names = fd['DATA'].attrs['dset_names']
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except:
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dset_names = [_ for _ in fd['DATA']]
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for dset_name in dset_names:
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parameters[dset_name] = []
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views[dset_name] = []
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dset = output.add_dset(dset_name)
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dset.notes = fd['DATA'][dset_name].attrs['notes']
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for h5dset in fd['DATA'][dset_name]:
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try:
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col_names = fd['DATA'][dset_name].attrs['col_names']
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except:
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col_names = [_ for _ in fd['DATA'][dset_name]]
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for h5dset in col_names:
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dset.add_columns(**{h5dset: fd['DATA'][dset_name][h5dset][...]})
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try:
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@ -870,10 +905,19 @@ class _DataSetView(object):
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data.append(values)
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return data
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def get_figure(self):
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def plot(self):
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f = self.get_figure(backend='plt')
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return f, f.get_axes()[0]
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def get_figure(self, backend=None):
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opts = self._plotopts
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figure = Figure(figsize=(3,2))
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if backend is None:
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figure = Figure()
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else:
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figure = plt.figure(num="[{}][{}]".format(self.dataset.title, self.title))
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axes = None
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proj = opts['projection']
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scale = opts['scale']
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@ -1113,7 +1157,7 @@ if has_gui:
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self.notebooks[dset.title] = nb
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#self.GetSizer().Add(nb, 1, wx.ALL|wx.EXPAND)
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self.GetSizer().Add(nb, proportion=1, flag=wx.ALL|wx.EXPAND)
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for view in dset.views():
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for view in dset.get_views():
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self.create_page(nb, view)
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self.create_menu()
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@ -1291,6 +1335,10 @@ if has_gui:
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self.Layout()
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self.update_statusbar()
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self._current_dset = name
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has_cluster = True if self.data[self._current_dset].get_cluster() is not None else False
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menu_item = self.GetMenuBar().FindItemById(302)
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menu_item.Enable(has_cluster)
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def create_page(self, nb, view):
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# Get the matplotlib figure
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@ -1324,95 +1372,6 @@ if has_gui:
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nb.AddPage(p, view.title)
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canvas.draw()
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def OLDcreate_page(self, nb, view):
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opts = view._plotopts
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p = wx.Panel(nb, -1)
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figure = Figure()
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axes = None
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proj = opts['projection']
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scale = opts['scale']
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if proj == 'rectilinear':
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axes = figure.add_subplot(111, projection='rectilinear')
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elif proj in ('polar', 'ortho', 'stereo'):
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axes = figure.add_subplot(111, projection='polar')
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canvas = FigureCanvas(p, -1, figure)
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sizer = wx.BoxSizer(wx.VERTICAL)
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toolbar = NavigationToolbar2WxAgg(canvas)
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toolbar.Realize()
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sizer.Add(toolbar, 0, wx.ALL|wx.EXPAND)
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toolbar.update()
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sizer.Add(canvas, 5, wx.ALL|wx.EXPAND)
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p.SetSizer(sizer)
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p.Fit()
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p.Show()
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for values, label in zip(view.get_data(), opts['legend']):
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# if we have only one column to plot, select a bar graph
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if np.shape(values)[0] == 1:
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xvalues = list(range(len(values[0])))
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axes.bar(xvalues, values[0], label=label,
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picker=5)
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axes.set_xticks(xvalues)
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else:
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if proj in ('ortho', 'stereo'):
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theta, phi, Xsec = cols2matrix(*values)
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theta_ticks = np.arange(0, 91, 15)
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if proj == 'ortho':
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R = np.sin(np.radians(theta))
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R_ticks = np.sin(np.radians(theta_ticks))
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elif proj == 'stereo':
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R = 2 * np.tan(np.radians(theta/2.))
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R_ticks = 2 * np.tan(np.radians(theta_ticks/2.))
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#R = np.tan(np.radians(theta/2.))
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X, Y = np.meshgrid(np.radians(phi), R)
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im = axes.pcolormesh(X, Y, Xsec)
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axes.set_yticks(R_ticks)
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axes.set_yticklabels(theta_ticks)
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figure.colorbar(im)
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elif proj == 'polar':
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values[0] = np.radians(values[0])
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axes.plot(*values, label=label, picker=5,
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marker=opts['marker'])
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else:
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if scale == 'semilogx':
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pltcmd = axes.semilogx
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elif scale == 'semilogy':
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pltcmd = axes.semilogy
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elif scale == 'log':
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pltcmd = axes.loglog
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else:
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pltcmd = axes.plot
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pltcmd(*values, label=label, picker=5,
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marker=opts['marker'])
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axes.grid(opts['grid'])
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axes.set_title(opts['title'])
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axes.set_xlabel(opts['xlabel'])
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axes.set_ylabel(opts['ylabel'])
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axes.set_xlim(*opts['xlim'])
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axes.set_ylim(*opts['ylim'])
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if label:
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axes.legend()
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axes.autoscale(enable=opts['autoscale'])
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# MPL events
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figure.canvas.mpl_connect('motion_notify_event', self.on_mpl_motion)
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figure.canvas.mpl_connect('pick_event', self.on_mpl_pick)
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nb.AddPage(p, view.title)
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def update_statusbar(self):
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sb = self.GetStatusBar()
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menu_id = self.GetMenuBar().FindMenu('Datasets')
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