Fix the stereographic projection issue.
The matplotlib function changed. A new keyword is needed to make the plotting "pcolormesh" function works. This keyword is "shading='gouraud'"
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@ -889,7 +889,7 @@ class _DataSetView(object):
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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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im = axes.pcolormesh(X, Y, Xsec, shading='gouraud')
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axes.set_yticks(R_ticks)
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axes.set_yticklabels(theta_ticks)
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@ -235,8 +235,8 @@ class DataSet(object):
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float: '{:<20.10e}', complex: 's'}
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self._formats = ((np.integer, '{:<20d}'),
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(np.floating, '{:<20.10e}'),
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(np.complex, '({0.real:<.10e} {0.imag:<.10e}j)'),
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(np.bool, '{:s}'),
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(complex, '({0.real:<.10e} {0.imag:<.10e}j)'),
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(bool, '{:s}'),
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(str, '{:s}'))
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@ -450,9 +450,13 @@ class DataSet(object):
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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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return ase.io.read(s, format='xyz')
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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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def select(self, *args, **kwargs):
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@ -785,13 +789,13 @@ class Data(object):
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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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dset.add_columns(**{h5dset: fd['DATA'][dset_name][h5dset].value})
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dset.add_columns(**{h5dset: fd['DATA'][dset_name][h5dset][...]})
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try:
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vfile = LooseVersion(fd['MsSpec viewer metainfo'].attrs['version'])
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if vfile > LooseVersion(msspec.__version__):
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raise NameError('File was saved with a more recent format')
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xml = fd['MsSpec viewer metainfo']['info'].value.tostring()
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xml = fd['MsSpec viewer metainfo']['info'][...].tobytes()
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root = etree.fromstring(xml)
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for elt0 in root.iter('parameters'):
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dset_name = elt0.attrib['dataset']
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@ -854,7 +858,7 @@ class Data(object):
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#win.show()
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#Gtk.main()
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app = _Application(self)
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exit_status = app.run(sys.argv)
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exit_status = app.run()#sys.argv)
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sys.exit(exit_status)
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class _Application(Gtk.Application):
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@ -947,7 +951,8 @@ class _DataSetView(object):
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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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# picker=5
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)
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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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@ -961,7 +966,7 @@ class _DataSetView(object):
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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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im = axes.pcolormesh(X, Y, Xsec, shading='gouraud')
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axes.set_yticks(R_ticks)
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axes.set_yticklabels(theta_ticks)
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@ -969,7 +974,7 @@ class _DataSetView(object):
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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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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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@ -980,7 +985,7 @@ class _DataSetView(object):
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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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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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@ -988,6 +993,7 @@ class _DataSetView(object):
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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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#axes.set_pickradius(5)
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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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@ -1242,7 +1248,7 @@ class _DataWindow(Gtk.ApplicationWindow):
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def on_close(self, action, param):
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if self.data.is_dirty():
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dlg = Gtk.Dialog(title="Warning: Unsaved data",
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transient_for=self, flags=Gtk.DialogFlags.MODAL)
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transient_for=self, modal=True)
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dlg.add_buttons(Gtk.STOCK_YES, Gtk.ResponseType.YES,
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Gtk.STOCK_NO, Gtk.ResponseType.NO)
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dlg.set_default_size(150, 100)
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@ -1474,9 +1480,14 @@ class OLD_DataWindow(wx.Frame):
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cluster_viewer = ClusterViewer(win, size=wx.Size(480, 340))
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dset = self.data[self._current_dset]
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s = StringIO()
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s.write(dset.get_parameter(group='Cluster', name='cluster')['value'])
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atoms = ase.io.read(s, format='xyz')
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#s = StringIO()
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#s.write(dset.get_parameter(group='Cluster', name='cluster')['value'])
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#_s = dset.get_parameter(group='Cluster', name='cluster')['value']
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#print(_s)
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# rewind to the begining of the string
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#s.seek(0)
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#atoms = ase.io.read(s, format='xyz')
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atoms = dset.get_cluster()
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cluster_viewer.set_atoms(atoms, rescale=True, center=True)
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cluster_viewer.rotate_atoms(0., 180.)
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cluster_viewer.rotate_atoms(-45., -45.)
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@ -1677,7 +1688,7 @@ class OLD_DataWindow(wx.Frame):
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if __name__ == "__main__":
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if True:
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if False:
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data = Data('all my data')
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dset = data.add_dset('Dataset 0')
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X = np.arange(0, 20)
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@ -1713,6 +1724,7 @@ if __name__ == "__main__":
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view.select('x', 'y')
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data.view()
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#import sys
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#data = Data.load(sys.argv[1])
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#data.view()
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exit()
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import sys
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data = Data.load(sys.argv[1])
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data.view()
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