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msspec_python3
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Code Issues 6 Pull Requests Releases Wiki Activity

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'"
This commit is contained in:
Sylvain Tricot 2023-12-01 10:19:22 +01:00
parent de70cc04a1
commit af72a764e5
2 changed files with 31 additions and 19 deletions
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2
src/msspec/iodata.py
View File

@ -889,7 +889,7 @@ class _DataSetView(object):
R_ticks = 2 * np.tan(np.radians(theta_ticks/2.)) R_ticks = 2 * np.tan(np.radians(theta_ticks/2.))
#R = np.tan(np.radians(theta/2.)) #R = np.tan(np.radians(theta/2.))
X, Y = np.meshgrid(np.radians(phi), R) X, Y = np.meshgrid(np.radians(phi), R)
im = axes.pcolormesh(X, Y, Xsec) im = axes.pcolormesh(X, Y, Xsec, shading='gouraud')
axes.set_yticks(R_ticks) axes.set_yticks(R_ticks)
axes.set_yticklabels(theta_ticks) axes.set_yticklabels(theta_ticks)

48
src/msspec/iodata_gi.py
View File

@ -235,8 +235,8 @@ class DataSet(object):
float: '{:<20.10e}', complex: 's'} float: '{:<20.10e}', complex: 's'}
self._formats = ((np.integer, '{:<20d}'), self._formats = ((np.integer, '{:<20d}'),
(np.floating, '{:<20.10e}'), (np.floating, '{:<20.10e}'),
(np.complex, '({0.real:<.10e} {0.imag:<.10e}j)'), (complex, '({0.real:<.10e} {0.imag:<.10e}j)'),
(np.bool, '{:s}'), (bool, '{:s}'),
(str, '{:s}')) (str, '{:s}'))
@ -450,9 +450,13 @@ class DataSet(object):
:return: The cluster :return: The cluster
:rtype: :py:class:`ase.Atoms` :rtype: :py:class:`ase.Atoms`
""" """
p = self.get_parameter(group='Cluster', name='cluster')['value']
s = StringIO() s = StringIO()
s.write(self.get_parameter(group='Cluster', name='cluster')['value']) s.write(self.get_parameter(group='Cluster', name='cluster')['value'])
return ase.io.read(s, format='xyz') s.seek(0)
#return ase.io.read(s, format='xyz')
cluster = list(read_xyz(s))[-1]
return cluster
def select(self, *args, **kwargs): def select(self, *args, **kwargs):
@ -785,13 +789,13 @@ class Data(object):
dset = output.add_dset(dset_name) dset = output.add_dset(dset_name)
dset.notes = fd['DATA'][dset_name].attrs['notes'] dset.notes = fd['DATA'][dset_name].attrs['notes']
for h5dset in fd['DATA'][dset_name]: for h5dset in fd['DATA'][dset_name]:
dset.add_columns(**{h5dset: fd['DATA'][dset_name][h5dset].value}) dset.add_columns(**{h5dset: fd['DATA'][dset_name][h5dset][...]})
try: try:
vfile = LooseVersion(fd['MsSpec viewer metainfo'].attrs['version']) vfile = LooseVersion(fd['MsSpec viewer metainfo'].attrs['version'])
if vfile > LooseVersion(msspec.__version__): if vfile > LooseVersion(msspec.__version__):
raise NameError('File was saved with a more recent format') raise NameError('File was saved with a more recent format')
xml = fd['MsSpec viewer metainfo']['info'].value.tostring() xml = fd['MsSpec viewer metainfo']['info'][...].tobytes()
root = etree.fromstring(xml) root = etree.fromstring(xml)
for elt0 in root.iter('parameters'): for elt0 in root.iter('parameters'):
dset_name = elt0.attrib['dataset'] dset_name = elt0.attrib['dataset']
@ -854,7 +858,7 @@ class Data(object):
#win.show() #win.show()
#Gtk.main() #Gtk.main()
app = _Application(self) app = _Application(self)
exit_status = app.run(sys.argv) exit_status = app.run()#sys.argv)
sys.exit(exit_status) sys.exit(exit_status)
class _Application(Gtk.Application): class _Application(Gtk.Application):
@ -947,7 +951,8 @@ class _DataSetView(object):
if np.shape(values)[0] == 1: if np.shape(values)[0] == 1:
xvalues = list(range(len(values[0]))) xvalues = list(range(len(values[0])))
axes.bar(xvalues, values[0], label=label, axes.bar(xvalues, values[0], label=label,
picker=5) # picker=5
)
axes.set_xticks(xvalues) axes.set_xticks(xvalues)
else: else:
if proj in ('ortho', 'stereo'): if proj in ('ortho', 'stereo'):
@ -961,7 +966,7 @@ class _DataSetView(object):
R_ticks = 2 * np.tan(np.radians(theta_ticks/2.)) R_ticks = 2 * np.tan(np.radians(theta_ticks/2.))
#R = np.tan(np.radians(theta/2.)) #R = np.tan(np.radians(theta/2.))
X, Y = np.meshgrid(np.radians(phi), R) X, Y = np.meshgrid(np.radians(phi), R)
im = axes.pcolormesh(X, Y, Xsec) im = axes.pcolormesh(X, Y, Xsec, shading='gouraud')
axes.set_yticks(R_ticks) axes.set_yticks(R_ticks)
axes.set_yticklabels(theta_ticks) axes.set_yticklabels(theta_ticks)
@ -969,7 +974,7 @@ class _DataSetView(object):
elif proj == 'polar': elif proj == 'polar':
values[0] = np.radians(values[0]) values[0] = np.radians(values[0])
axes.plot(*values, label=label, picker=5, axes.plot(*values, label=label, #picker=5,
marker=opts['marker']) marker=opts['marker'])
else: else:
if scale == 'semilogx': if scale == 'semilogx':
@ -980,7 +985,7 @@ class _DataSetView(object):
pltcmd = axes.loglog pltcmd = axes.loglog
else: else:
pltcmd = axes.plot pltcmd = axes.plot
pltcmd(*values, label=label, picker=5, pltcmd(*values, label=label, #picker=5,
marker=opts['marker']) marker=opts['marker'])
axes.grid(opts['grid']) axes.grid(opts['grid'])
axes.set_title(opts['title']) axes.set_title(opts['title'])
@ -988,6 +993,7 @@ class _DataSetView(object):
axes.set_ylabel(opts['ylabel']) axes.set_ylabel(opts['ylabel'])
axes.set_xlim(*opts['xlim']) axes.set_xlim(*opts['xlim'])
axes.set_ylim(*opts['ylim']) axes.set_ylim(*opts['ylim'])
#axes.set_pickradius(5)
if label: if label:
axes.legend() axes.legend()
axes.autoscale(enable=opts['autoscale']) axes.autoscale(enable=opts['autoscale'])
@ -1242,7 +1248,7 @@ class _DataWindow(Gtk.ApplicationWindow):
def on_close(self, action, param): def on_close(self, action, param):
if self.data.is_dirty(): if self.data.is_dirty():
dlg = Gtk.Dialog(title="Warning: Unsaved data", dlg = Gtk.Dialog(title="Warning: Unsaved data",
transient_for=self, flags=Gtk.DialogFlags.MODAL) transient_for=self, modal=True)
dlg.add_buttons(Gtk.STOCK_YES, Gtk.ResponseType.YES, dlg.add_buttons(Gtk.STOCK_YES, Gtk.ResponseType.YES,
Gtk.STOCK_NO, Gtk.ResponseType.NO) Gtk.STOCK_NO, Gtk.ResponseType.NO)
dlg.set_default_size(150, 100) dlg.set_default_size(150, 100)
@ -1474,9 +1480,14 @@ class OLD_DataWindow(wx.Frame):
cluster_viewer = ClusterViewer(win, size=wx.Size(480, 340)) cluster_viewer = ClusterViewer(win, size=wx.Size(480, 340))
dset = self.data[self._current_dset] dset = self.data[self._current_dset]
s = StringIO() #s = StringIO()
s.write(dset.get_parameter(group='Cluster', name='cluster')['value']) #s.write(dset.get_parameter(group='Cluster', name='cluster')['value'])
atoms = ase.io.read(s, format='xyz') #_s = dset.get_parameter(group='Cluster', name='cluster')['value']
#print(_s)
# rewind to the begining of the string
#s.seek(0)
#atoms = ase.io.read(s, format='xyz')
atoms = dset.get_cluster()
cluster_viewer.set_atoms(atoms, rescale=True, center=True) cluster_viewer.set_atoms(atoms, rescale=True, center=True)
cluster_viewer.rotate_atoms(0., 180.) cluster_viewer.rotate_atoms(0., 180.)
cluster_viewer.rotate_atoms(-45., -45.) cluster_viewer.rotate_atoms(-45., -45.)
@ -1677,7 +1688,7 @@ class OLD_DataWindow(wx.Frame):
if __name__ == "__main__": if __name__ == "__main__":
if True: if False:
data = Data('all my data') data = Data('all my data')
dset = data.add_dset('Dataset 0') dset = data.add_dset('Dataset 0')
X = np.arange(0, 20) X = np.arange(0, 20)
@ -1713,6 +1724,7 @@ if __name__ == "__main__":
view.select('x', 'y') view.select('x', 'y')
data.view() data.view()
#import sys exit()
#data = Data.load(sys.argv[1]) import sys
#data.view() data = Data.load(sys.argv[1])
data.view()