class XASNormPanel(TaskPanel):
"""XAS normalization Panel"""
def __init__(self, parent, controller=None, **kws):
TaskPanel.__init__(self,
parent,
controller,
configname='xasnorm_config',
config=defaults,
**kws)
def build_display(self):
panel = self.panel
self.wids = {}
self.plotone_op = Choice(panel,
choices=list(PlotOne_Choices.keys()),
action=self.onPlotOne,
size=(200, -1))
self.plotsel_op = Choice(panel,
choices=list(PlotSel_Choices.keys()),
action=self.onPlotSel,
size=(200, -1))
self.plotone_op.SetSelection(1)
self.plotsel_op.SetSelection(1)
plot_one = Button(panel,
'Plot Current Group',
size=(170, -1),
action=self.onPlotOne)
plot_sel = Button(panel,
'Plot Selected Groups',
size=(170, -1),
action=self.onPlotSel)
e0panel = wx.Panel(panel)
self.wids['auto_e0'] = Check(e0panel,
default=True,
label='auto?',
action=self.onSet_XASE0)
self.wids['showe0'] = Check(e0panel,
default=True,
label='show?',
action=self.onSet_XASE0)
sx = wx.BoxSizer(wx.HORIZONTAL)
sx.Add(self.wids['auto_e0'], 0, LEFT, 4)
sx.Add(self.wids['showe0'], 0, LEFT, 4)
pack(e0panel, sx)
self.wids['auto_step'] = Check(panel,
default=True,
label='auto?',
action=self.onNormMethod)
self.wids['nvict'] = Choice(panel,
choices=('0', '1', '2', '3'),
size=(100, -1),
action=self.onNormMethod,
default=0)
self.wids['nnorm'] = Choice(panel,
choices=list(Nnorm_choices.values()),
size=(100, -1),
action=self.onNormMethod,
default=0)
opts = {
'size': (100, -1),
'digits': 2,
'increment': 5.0,
'action': self.onSet_Ranges
}
xas_pre1 = self.add_floatspin('pre1', value=defaults['pre1'], **opts)
xas_pre2 = self.add_floatspin('pre2', value=defaults['pre2'], **opts)
xas_norm1 = self.add_floatspin('norm1',
value=defaults['norm1'],
**opts)
xas_norm2 = self.add_floatspin('norm2',
value=defaults['norm2'],
**opts)
opts = {'digits': 3, 'increment': 0.1, 'value': 0}
plot_voff = self.add_floatspin('plot_voff',
with_pin=False,
size=(80, -1),
action=self.onVoffset,
**opts)
xas_e0 = self.add_floatspin('e0', action=self.onSet_XASE0Val, **opts)
xas_step = self.add_floatspin('step',
action=self.onSet_XASStep,
with_pin=False,
min_val=0.0,
**opts)
opts['value'] = 1.0
scale = self.add_floatspin('scale', action=self.onSet_Scale, **opts)
self.wids['norm_method'] = Choice(
panel,
choices=('polynomial', 'mback'), # , 'area'),
size=(120, -1),
action=self.onNormMethod)
self.wids['norm_method'].SetSelection(0)
atsyms = ['?'] + self.larch.symtable._xray._xraydb.atomic_symbols
edges = ('K', 'L3', 'L2', 'L1', 'M5')
self.wids['atsym'] = Choice(panel, choices=atsyms, size=(75, -1))
self.wids['edge'] = Choice(panel, choices=edges, size=(60, -1))
self.wids['is_frozen'] = Check(panel,
default=False,
label='Freeze Group',
action=self.onFreezeGroup)
saveconf = Button(panel,
'Save as Default Settings',
size=(200, -1),
action=self.onSaveConfigBtn)
use_auto = Button(panel,
'Use Default Settings',
size=(200, -1),
action=self.onAutoNorm)
copy_auto = Button(panel,
'Copy',
size=(60, -1),
action=self.onCopyAuto)
def CopyBtn(name):
return Button(panel,
'Copy',
size=(60, -1),
action=partial(self.onCopyParam, name))
add_text = self.add_text
HLINEWID = 575
panel.Add(SimpleText(panel,
'XAS Pre-edge subtraction and Normalization',
**self.titleopts),
dcol=4)
panel.Add(SimpleText(panel, 'Copy to Selected Groups:'),
style=RIGHT,
dcol=2)
panel.Add(plot_sel, newrow=True)
panel.Add(self.plotsel_op, dcol=3)
panel.Add(SimpleText(panel, 'Y Offset:'), style=RIGHT)
panel.Add(plot_voff, style=RIGHT)
panel.Add(plot_one, newrow=True)
panel.Add(self.plotone_op, dcol=4)
panel.Add(CopyBtn('plotone_op'), dcol=1, style=RIGHT)
panel.Add(HLine(panel, size=(HLINEWID, 3)), dcol=6, newrow=True)
add_text('Non-XAS Data Scale:')
panel.Add(scale, dcol=2)
panel.Add(HLine(panel, size=(HLINEWID, 3)), dcol=6, newrow=True)
add_text('XAS Data:')
panel.Add(use_auto, dcol=4)
panel.Add(copy_auto, dcol=1, style=RIGHT)
add_text('Element and Edge: ', newrow=True)
panel.Add(self.wids['atsym'])
panel.Add(self.wids['edge'], dcol=3)
panel.Add(CopyBtn('atsym'), dcol=1, style=RIGHT)
add_text('E0 : ')
panel.Add(xas_e0)
panel.Add(e0panel, dcol=3)
panel.Add(CopyBtn('xas_e0'), dcol=1, style=RIGHT)
add_text('Edge Step: ')
panel.Add(xas_step)
panel.Add(self.wids['auto_step'], dcol=3)
panel.Add(CopyBtn('xas_step'), dcol=1, style=RIGHT)
panel.Add((5, 5), newrow=True)
panel.Add(HLine(panel, size=(HLINEWID, 3)), dcol=6, newrow=True)
add_text('Pre-edge range: ')
panel.Add(xas_pre1)
add_text(' : ', newrow=False)
panel.Add(xas_pre2, dcol=2)
panel.Add(CopyBtn('xas_pre'), dcol=1, style=RIGHT)
panel.Add(SimpleText(panel, 'Victoreen order:'), newrow=True)
panel.Add(self.wids['nvict'], dcol=4)
panel.Add((5, 5), newrow=True)
panel.Add(HLine(panel, size=(HLINEWID, 3)), dcol=6, newrow=True)
add_text('Normalization method: ')
panel.Add(self.wids['norm_method'], dcol=4)
panel.Add(CopyBtn('xas_norm'), dcol=1, style=RIGHT)
add_text('Normalization range: ')
panel.Add(xas_norm1)
add_text(' : ', newrow=False)
panel.Add(xas_norm2, dcol=2)
panel.Add(SimpleText(panel, 'Polynomial Type:'), newrow=True)
panel.Add(self.wids['nnorm'], dcol=4)
panel.Add(HLine(panel, size=(HLINEWID, 3)), dcol=6, newrow=True)
panel.Add((5, 5), newrow=True)
panel.Add(self.wids['is_frozen'], newrow=True)
panel.Add(saveconf, dcol=5)
panel.Add((5, 5), newrow=True)
panel.Add(HLine(panel, size=(HLINEWID, 3)), dcol=6, newrow=True)
panel.pack()
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add((5, 5), 0, LEFT, 3)
sizer.Add(panel, 0, LEFT, 3)
sizer.Add((5, 5), 0, LEFT, 3)
pack(self, sizer)
def get_config(self, dgroup=None):
"""custom get_config to possibly inherit from Athena settings"""
if dgroup is None:
dgroup = self.controller.get_group()
if dgroup is None:
return self.get_defaultconfig()
if hasattr(dgroup, self.configname):
conf = getattr(dgroup, self.configname)
else:
conf = self.get_defaultconfig()
if hasattr(dgroup, 'bkg_params'): # from Athena
for attr in ('e0', 'pre1', 'pre2', 'nnorm'):
conf[attr] = getattr(dgroup.bkg_params, attr, conf[attr])
for attr, aattr in (('norm1', 'nor1'), ('norm2', 'nor2')):
conf[attr] = getattr(dgroup.bkg_params, aattr, conf[attr])
conf['auto_step'] = (float(
getattr(dgroup.bkg_params, 'fixstep', 0.0)) < 0.5)
conf['edge_step'] = getattr(dgroup.bkg_params, 'step',
conf['edge_step'])
if conf['edge_step'] is None:
conf['edge_step'] = getattr(dgroup, 'edge_step', conf['edge_step'])
conf['atsym'] = getattr(dgroup, 'atsym', conf['atsym'])
conf['edge'] = getattr(dgroup, 'edge', conf['edge'])
if hasattr(dgroup, 'e0') and conf['atsym'] == '?':
atsym, edge = guess_edge(dgroup.e0)
conf['atsym'] = atsym
conf['edge'] = edge
if hasattr(dgroup, 'mback_params'):
conf['atsym'] = getattr(dgroup.mback_params, 'atsym',
conf['atsym'])
conf['edge'] = getattr(dgroup.mback_params, 'edge', conf['edge'])
setattr(dgroup, self.configname, conf)
return conf
def fill_form(self, dgroup):
"""fill in form from a data group"""
opts = self.get_config(dgroup)
self.skip_process = True
if dgroup.datatype == 'xas':
self.plotone_op.SetChoices(list(PlotOne_Choices.keys()))
self.plotsel_op.SetChoices(list(PlotSel_Choices.keys()))
self.plotone_op.SetStringSelection(opts['plotone_op'])
self.plotsel_op.SetStringSelection(opts['plotsel_op'])
self.wids['e0'].SetValue(opts['e0'])
edge_step = opts.get('edge_step', None)
if edge_step is None:
edge_step = 1.0
if hasattr(dgroup, 'e0') and opts['atsym'] == '?':
atsym, edge = guess_edge(dgroup.e0)
opts['atsym'] = atsym
opts['edge'] = edge
self.wids['step'].SetValue(edge_step)
autoset_fs_increment(self.wids['step'], edge_step)
for attr in ('pre1', 'pre2', 'norm1', 'norm2'):
val = opts.get(attr, None)
if val is not None:
self.wids[attr].SetValue(val)
self.set_nnorm_widget(opts.get('nnorm'))
self.wids['nvict'].SetSelection(opts['nvict'])
self.wids['showe0'].SetValue(opts['show_e0'])
self.wids['auto_e0'].SetValue(opts['auto_e0'])
self.wids['auto_step'].SetValue(opts['auto_step'])
self.wids['edge'].SetStringSelection(opts['edge'].title())
self.wids['atsym'].SetStringSelection(opts['atsym'].title())
self.wids['norm_method'].SetStringSelection(
opts['norm_method'].lower())
for attr in ('pre1', 'pre2', 'norm1', 'norm2', 'nnorm', 'edge',
'atsym', 'step', 'norm_method'):
self.wids[attr].Enable()
self.wids['scale'].Disable()
else:
self.plotone_op.SetChoices(list(PlotOne_Choices_nonxas.keys()))
self.plotsel_op.SetChoices(list(PlotSel_Choices_nonxas.keys()))
self.wids['scale'].SetValue(opts['scale'])
for attr in ('pre1', 'pre2', 'norm1', 'norm2', 'nnorm', 'edge',
'atsym', 'step', 'norm_method'):
self.wids[attr].Disable()
self.wids['scale'].Enable()
frozen = opts.get('is_frozen', False)
if hasattr(dgroup, 'is_frozen'):
frozen = dgroup.is_frozen
self.wids['is_frozen'].SetValue(frozen)
self._set_frozen(frozen)
wx.CallAfter(self.unset_skip_process)
def set_nnorm_widget(self, nnorm=None):
if nnorm is None:
nnorm_str = 'auto'
else:
try:
nnorm = int(nnorm)
except ValueError:
nnorm = None
nnorm_str = Nnorm_choices.get(nnorm, 'auto')
self.wids['nnorm'].SetStringSelection(nnorm_str)
def unset_skip_process(self):
self.skip_process = False
def read_form(self):
"read form, return dict of values"
form_opts = {}
form_opts['e0'] = self.wids['e0'].GetValue()
form_opts['edge_step'] = self.wids['step'].GetValue()
for attr in ('pre1', 'pre2', 'norm1', 'norm2'):
val = self.wids[attr].GetValue()
if val == 0: val = None
form_opts[attr] = val
form_opts['nnorm'] = Nnorm_names.get(
self.wids['nnorm'].GetStringSelection(), None)
form_opts['nvict'] = int(self.wids['nvict'].GetSelection())
form_opts['plotone_op'] = self.plotone_op.GetStringSelection()
form_opts['plotsel_op'] = self.plotsel_op.GetStringSelection()
form_opts['plot_voff'] = self.wids['plot_voff'].GetValue()
form_opts['show_e0'] = self.wids['showe0'].IsChecked()
form_opts['auto_e0'] = self.wids['auto_e0'].IsChecked()
form_opts['auto_step'] = self.wids['auto_step'].IsChecked()
form_opts['norm_method'] = self.wids['norm_method'].GetStringSelection(
).lower()
form_opts['edge'] = self.wids['edge'].GetStringSelection().title()
form_opts['atsym'] = self.wids['atsym'].GetStringSelection().title()
form_opts['scale'] = self.wids['scale'].GetValue()
return form_opts
def onNormMethod(self, evt=None):
method = self.wids['norm_method'].GetStringSelection().lower()
self.update_config({'norm_method': method})
if method.startswith('mback'):
dgroup = self.controller.get_group()
cur_elem = self.wids['atsym'].GetStringSelection()
if hasattr(dgroup, 'e0') and cur_elem == 'H':
atsym, edge = guess_edge(dgroup.e0)
self.wids['edge'].SetStringSelection(edge)
self.wids['atsym'].SetStringSelection(atsym)
self.update_config({'edge': edge, 'atsym': atsym})
time.sleep(0.01)
wx.CallAfter(self.onReprocess)
def _set_frozen(self, frozen):
try:
dgroup = self.controller.get_group()
dgroup.is_frozen = frozen
except:
pass
for wattr in ('e0', 'step', 'pre1', 'pre2', 'norm1', 'norm2', 'nvict',
'nnorm', 'showe0', 'auto_e0', 'auto_step', 'norm_method',
'edge', 'atsym'):
self.wids[wattr].Enable(not frozen)
def onFreezeGroup(self, evt=None):
self._set_frozen(evt.IsChecked())
def onPlotOne(self, evt=None):
self.plot(self.controller.get_group())
def onVoffset(self, evt=None):
time.sleep(0.01)
wx.CallAfter(self.onPlotSel)
def onPlotSel(self, evt=None):
newplot = True
group_ids = self.controller.filelist.GetCheckedStrings()
if len(group_ids) < 1:
return
last_id = group_ids[-1]
groupname = self.controller.file_groups[str(last_id)]
dgroup = self.controller.get_group(groupname)
plot_choices = PlotSel_Choices
if dgroup.datatype != 'xas':
plot_choices = PlotSel_Choices_nonxas
ytitle = self.plotsel_op.GetStringSelection()
yarray_name = plot_choices[ytitle]
ylabel = getattr(plotlabels, yarray_name, ytitle)
if yarray_name == 'norm':
norm_method = self.wids['norm_method'].GetStringSelection().lower()
if norm_method.startswith('mback'):
yarray_name = 'norm_mback'
ylabel = "%s (MBACK)" % ylabel
elif norm_method.startswith('area'):
yarray_name = 'norm_area'
ylabel = "%s (Area)" % ylabel
voff = self.wids['plot_voff'].GetValue()
for ix, checked in enumerate(group_ids):
yoff = ix * voff
groupname = self.controller.file_groups[str(checked)]
dgroup = self.controller.get_group(groupname)
plot_yarrays = [(yarray_name, PLOTOPTS_1, dgroup.filename)]
if dgroup is not None:
dgroup.plot_extras = []
self.plot(dgroup,
title='',
new=newplot,
multi=True,
yoff=yoff,
plot_yarrays=plot_yarrays,
with_extras=False,
delay_draw=True)
newplot = False
ppanel = self.controller.get_display(stacked=False).panel
ppanel.conf.show_legend = True
ppanel.conf.draw_legend()
ppanel.unzoom_all()
def onAutoNorm(self, evt=None):
dgroup = self.controller.get_group()
try:
norm2 = max(dgroup.energy) - dgroup.e0
norm1 = 5.0 * int(norm2 / 15.0)
nnorm = 2
if (norm2 - norm1 < 350): nnorm = 1
if (norm2 - norm1 < 50): nnorm = 0
except:
nnorm = None
self.wids['auto_step'].SetValue(1)
self.wids['auto_e0'].SetValue(1)
self.wids['nvict'].SetSelection(0)
self.wids['pre1'].SetValue(0)
self.wids['pre2'].SetValue(0)
self.wids['norm1'].SetValue(0)
self.wids['norm2'].SetValue(0)
if nnorm is not None:
self.set_nnorm_widget(nnorm)
self.wids['norm_method'].SetSelection(0)
self.onReprocess()
def onCopyAuto(self, evt=None):
opts = dict(pre1=0,
pre2=0,
nvict=0,
norm1=0,
norm2=0,
norm_method='polynomial',
nnorm=2,
auto_e0=1,
auto_step=1)
for checked in self.controller.filelist.GetCheckedStrings():
groupname = self.controller.file_groups[str(checked)]
grp = self.controller.get_group(groupname)
if grp != self.controller.group and not grp.is_frozen:
# try:
# norm2 = max(grp.energy) - grp.e0
# norm1 = 5.0*int(norm2/15.0)
# nnorm = 2
# if (norm2-norm1 < 350): nnorm = 1
# if (norm2-norm1 < 50): nnorm = 0
# except:
# nnorm = 1
# opts['nnorm'] = nnorm
self.update_config(opts, dgroup=grp)
self.fill_form(grp)
self.process(grp, noskip=True)
def onSaveConfigBtn(self, evt=None):
conf = self.get_config()
conf.update(self.read_form())
self.set_defaultconfig(conf)
def onCopyParam(self, name=None, evt=None):
conf = self.get_config()
form = self.read_form()
conf.update(form)
dgroup = self.controller.get_group()
self.update_config(conf)
self.fill_form(dgroup)
opts = {}
name = str(name)
def copy_attrs(*args):
for a in args:
opts[a] = conf[a]
if name == 'plotone_op':
copy_attrs('plotone_op')
elif name == 'xas_e0':
copy_attrs('e0', 'show_e0', 'auto_e0')
elif name == 'xas_step':
copy_attrs('edge_step', 'auto_step')
elif name == 'xas_pre':
copy_attrs('pre1', 'pre2', 'nvict')
elif name == 'atsym':
copy_attrs('atsym', 'edge')
elif name == 'xas_norm':
copy_attrs('norm_method', 'nnorm', 'norm1', 'norm2')
for checked in self.controller.filelist.GetCheckedStrings():
groupname = self.controller.file_groups[str(checked)]
grp = self.controller.get_group(groupname)
if grp != self.controller.group and not grp.is_frozen:
self.update_config(opts, dgroup=grp)
self.fill_form(grp)
self.process(grp, noskip=True)
def onSet_XASE0(self, evt=None, value=None):
"handle setting auto e0 / show e0"
auto_e0 = self.wids['auto_e0'].GetValue()
self.update_config({
'e0': self.wids['e0'].GetValue(),
'auto_e0': self.wids['auto_e0'].GetValue()
})
time.sleep(0.01)
wx.CallAfter(self.onReprocess)
def onSet_XASE0Val(self, evt=None, value=None):
"handle setting e0"
self.wids['auto_e0'].SetValue(0)
self.update_config({
'e0': self.wids['e0'].GetValue(),
'auto_e0': self.wids['auto_e0'].GetValue()
})
time.sleep(0.01)
wx.CallAfter(self.onReprocess)
def onSet_XASStep(self, evt=None, value=None):
"handle setting edge step"
edge_step = self.wids['step'].GetValue()
if edge_step < 0:
self.wids['step'].SetValue(abs(edge_step))
self.wids['auto_step'].SetValue(0)
self.update_config({'edge_step': abs(edge_step), 'auto_step': False})
autoset_fs_increment(self.wids['step'], abs(edge_step))
time.sleep(0.01)
wx.CallAfter(self.onReprocess)
def onSet_Scale(self, evt=None, value=None):
"handle setting non-XAFS scale value"
self.update_config({'scale': self.wids['scale'].GetValue()})
time.sleep(0.01)
wx.CallAfter(self.onReprocess)
def onSet_Ranges(self, evt=None, **kws):
conf = {}
for attr in ('pre1', 'pre2', 'norm1', 'norm2'):
conf[attr] = self.wids[attr].GetValue()
self.update_config(conf)
time.sleep(0.01)
wx.CallAfter(self.onReprocess)
def onSelPoint(self, evt=None, opt='__', relative_e0=True, win=None):
"""
get last selected point from a specified plot window
and fill in the value for the widget defined by `opt`.
by default it finds the latest cursor position from the
cursor history of the first 20 plot windows.
"""
if opt not in self.wids:
return None
_x, _y = last_cursor_pos(win=win, _larch=self.larch)
if _x is None:
return
e0 = self.wids['e0'].GetValue()
if opt == 'e0':
self.wids['e0'].SetValue(_x)
self.wids['auto_e0'].SetValue(0)
elif opt in ('pre1', 'pre2', 'norm1', 'norm2'):
self.wids[opt].SetValue(_x - e0)
time.sleep(0.01)
wx.CallAfter(self.onReprocess)
def onReprocess(self, evt=None, value=None, **kws):
"handle request reprocess"
if self.skip_process:
return
try:
dgroup = self.controller.get_group()
except TypeError:
return
if not hasattr(dgroup, self.configname):
return
form = self.read_form()
self.process(dgroup=dgroup)
self.plot(dgroup)
def make_dnormde(self, dgroup):
form = dict(group=dgroup.groupname)
self.larch_eval(
"{group:s}.dnormde={group:s}.dmude/{group:s}.edge_step".format(
**form))
def process(self, dgroup=None, force_mback=False, noskip=False, **kws):
""" handle process (pre-edge/normalize) of XAS data from XAS form
"""
if self.skip_process and not noskip:
return
if dgroup is None:
dgroup = self.controller.get_group()
if dgroup is None:
return
self.skip_process = True
conf = self.get_config(dgroup)
dgroup.custom_plotopts = {}
form = self.read_form()
form['group'] = dgroup.groupname
if dgroup.datatype != 'xas':
self.skip_process = False
dgroup.mu = dgroup.ydat * 1.0
opts = {'group': dgroup.groupname, 'scale': conf.get('scale', 1.0)}
self.larch_eval("{group:s}.scale = {scale:.8f}".format(**opts))
self.larch_eval(
"{group:s}.norm = {scale:.8f}*{group:s}.ydat".format(**opts))
return
en_units = getattr(dgroup, 'energy_units', None)
if en_units is None:
en_units = guess_energy_units(dgroup.energy)
if en_units != 'eV':
mono_dspace = getattr(dgroup, 'mono_dspace', 1)
dlg = EnergyUnitsDialog(self.parent,
dgroup.energy,
unitname=en_units,
dspace=mono_dspace)
res = dlg.GetResponse()
dlg.Destroy()
if res.ok:
en_units = res.units
dgroup.mono_dspace = res.dspace
dgroup.xdat = dgroup.energy = res.energy
dgroup.energy_units = en_units
e0 = form['e0']
edge_step = form['edge_step']
copts = [dgroup.groupname]
if not form['auto_e0']:
if e0 < max(dgroup.energy) and e0 > min(dgroup.energy):
copts.append("e0=%.4f" % float(e0))
if not form['auto_step']:
copts.append("step=%s" % gformat(float(edge_step)))
for attr in ('pre1', 'pre2', 'nvict', 'nnorm', 'norm1', 'norm2'):
if form[attr] is None:
copts.append("%s=None" % attr)
else:
copts.append("%s=%.2f" % (attr, form[attr]))
self.larch_eval("pre_edge(%s)" % (', '.join(copts)))
self.larch_eval(
"{group:s}.norm_poly = 1.0*{group:s}.norm".format(**form))
norm_method = form['norm_method'].lower()
form['normmeth'] = 'poly'
if force_mback or norm_method.startswith('mback'):
form['normmeth'] = 'mback'
copts = [dgroup.groupname]
copts.append("z=%d" % atomic_number(form['atsym']))
copts.append("edge='%s'" % form['edge'])
for attr in ('pre1', 'pre2', 'nvict', 'nnorm', 'norm1', 'norm2'):
if form[attr] is None:
copts.append("%s=None" % attr)
else:
copts.append("%s=%.2f" % (attr, form[attr]))
self.larch_eval("mback_norm(%s)" % (', '.join(copts)))
if form['auto_step']:
norm_expr = """{group:s}.norm = 1.0*{group:s}.norm_{normmeth:s}
{group:s}.edge_step = 1.0*{group:s}.edge_step_{normmeth:s}"""
self.larch_eval(norm_expr.format(**form))
else:
norm_expr = """{group:s}.norm = 1.0*{group:s}.norm_{normmeth:s}
{group:s}.norm *= {group:s}.edge_step_{normmeth:s}/{edge_step:.8f}"""
self.larch_eval(norm_expr.format(**form))
if norm_method.startswith('area'):
form['normmeth'] = 'area'
expr = """{group:s}.norm = 1.0*{group:s}.norm_{normmeth:s}
{group:s}.edge_step = 1.0*{group:s}.edge_step_{normmeth:s}"""
self.larch_eval(expr.format(**form))
self.make_dnormde(dgroup)
if form['auto_e0']:
self.wids['e0'].SetValue(dgroup.e0)
if form['auto_step']:
self.wids['step'].SetValue(dgroup.edge_step)
autoset_fs_increment(self.wids['step'], dgroup.edge_step)
self.wids['atsym'].SetStringSelection(dgroup.atsym)
self.wids['edge'].SetStringSelection(dgroup.edge)
self.set_nnorm_widget(dgroup.pre_edge_details.nnorm)
for attr in ('e0', 'edge_step'):
conf[attr] = getattr(dgroup, attr)
for attr in ('pre1', 'pre2', 'norm1', 'norm2'):
conf[attr] = val = getattr(dgroup.pre_edge_details, attr, None)
if val is not None:
self.wids[attr].SetValue(val)
if hasattr(dgroup, 'mback_params'): # from mback
conf['atsym'] = getattr(dgroup.mback_params, 'atsym')
conf['edge'] = getattr(dgroup.mback_params, 'edge')
self.update_config(conf, dgroup=dgroup)
wx.CallAfter(self.unset_skip_process)
def get_plot_arrays(self, dgroup):
lab = plotlabels.norm
if dgroup is None:
return
dgroup.plot_y2label = None
dgroup.plot_xlabel = plotlabels.energy
dgroup.plot_yarrays = [('norm', PLOTOPTS_1, lab)]
if dgroup.datatype != 'xas':
pchoice = PlotOne_Choices_nonxas[
self.plotone_op.GetStringSelection()]
dgroup.plot_xlabel = 'x'
dgroup.plot_ylabel = 'y'
dgroup.plot_yarrays = [('ydat', PLOTOPTS_1, 'ydat')]
dgroup.dmude = np.gradient(dgroup.ydat) / np.gradient(dgroup.xdat)
if not hasattr(dgroup, 'scale'):
dgroup.scale = 1.0
dgroup.norm = dgroup.ydat * dgroup.scale
if pchoice == 'dmude':
dgroup.plot_ylabel = 'dy/dx'
dgroup.plot_yarrays = [('dmude', PLOTOPTS_1, 'dy/dx')]
elif pchoice == 'norm':
dgroup.plot_ylabel = 'scaled y'
dgroup.plot_yarrays = [('norm', PLOTOPTS_1, 'y/scale')]
elif pchoice == 'norm+dnormde':
lab = plotlabels.norm
dgroup.plot_y2label = 'dy/dx'
dgroup.plot_yarrays = [('ydat', PLOTOPTS_1, 'y'),
('dnormde', PLOTOPTS_D, 'dy/dx')]
return
req_attrs = ['e0', 'norm', 'dmude', 'pre_edge']
pchoice = PlotOne_Choices[self.plotone_op.GetStringSelection()]
if pchoice in ('mu', 'norm', 'flat', 'dmude'):
lab = getattr(plotlabels, pchoice)
dgroup.plot_yarrays = [(pchoice, PLOTOPTS_1, lab)]
elif pchoice == 'prelines':
dgroup.plot_yarrays = [('mu', PLOTOPTS_1, plotlabels.mu),
('pre_edge', PLOTOPTS_2, 'pre edge'),
('post_edge', PLOTOPTS_2, 'post edge')]
elif pchoice == 'preedge':
lab = r'pre-edge subtracted $\mu$'
dgroup.pre_edge_sub = dgroup.norm * dgroup.edge_step
dgroup.plot_yarrays = [('pre_edge_sub', PLOTOPTS_1, lab)]
elif pchoice == 'mu+dmude':
lab = plotlabels.mu
lab2 = plotlabels.dmude
dgroup.plot_yarrays = [('mu', PLOTOPTS_1, lab),
('dmude', PLOTOPTS_D, lab2)]
dgroup.plot_y2label = lab2
elif pchoice == 'norm+dnormde':
lab = plotlabels.norm
lab2 = plotlabels.dmude + ' (normalized)'
dgroup.plot_yarrays = [('norm', PLOTOPTS_1, lab),
('dnormde', PLOTOPTS_D, lab2)]
dgroup.plot_y2label = lab2
elif pchoice == 'mback_norm':
req_attrs.append('mback_norm')
lab = r'$\mu$'
if not hasattr(dgroup, 'mback_mu'):
self.process(dgroup=dgroup, force_mback=True)
dgroup.plot_yarrays = [('mu', PLOTOPTS_1, lab),
('mback_mu', PLOTOPTS_2,
r'tabulated $\mu(E)$')]
elif pchoice == 'mback_poly':
req_attrs.append('mback_norm')
lab = plotlabels.norm
if not hasattr(dgroup, 'mback_mu'):
self.process(dgroup=dgroup, force_mback=True)
dgroup.plot_yarrays = [('norm_mback', PLOTOPTS_1, 'mback'),
('norm_poly', PLOTOPTS_2, 'polynomial')]
elif pchoice == 'area_norm':
dgroup.plot_yarrays = [('norm_area', PLOTOPTS_1, 'area'),
('norm_poly', PLOTOPTS_2, 'polynomial')]
dgroup.plot_ylabel = lab
needs_proc = False
for attr in req_attrs:
needs_proc = needs_proc or (not hasattr(dgroup, attr))
if needs_proc:
self.process(dgroup=dgroup, noskip=True)
y4e0 = dgroup.ydat = getattr(dgroup, dgroup.plot_yarrays[0][0],
dgroup.mu)
dgroup.plot_extras = []
if self.wids['showe0'].IsChecked():
ie0 = index_of(dgroup.energy, dgroup.e0)
dgroup.plot_extras.append(('marker', dgroup.e0, y4e0[ie0], {}))
def plot(self,
dgroup,
title=None,
plot_yarrays=None,
yoff=0,
delay_draw=False,
multi=False,
new=True,
zoom_out=True,
with_extras=True,
**kws):
if self.skip_plotting:
return
ppanel = self.controller.get_display(stacked=False).panel
viewlims = ppanel.get_viewlimits()
plotcmd = ppanel.oplot
if new:
plotcmd = ppanel.plot
groupname = getattr(dgroup, 'groupname', None)
if groupname is None:
return
if not hasattr(dgroup, 'xdat'):
print("Cannot plot group ", groupname)
if ((getattr(dgroup, 'plot_yarrays', None) is None
or getattr(dgroup, 'energy', None) is None
or getattr(dgroup, 'mu', None) is None
or getattr(dgroup, 'e0', None) is None
or getattr(dgroup, 'dmude', None) is None
or getattr(dgroup, 'norm', None) is None)):
self.process(dgroup=dgroup)
self.get_plot_arrays(dgroup)
if plot_yarrays is None and hasattr(dgroup, 'plot_yarrays'):
plot_yarrays = dgroup.plot_yarrays
popts = kws
path, fname = os.path.split(dgroup.filename)
if 'label' not in popts:
popts['label'] = dgroup.plot_ylabel
zoom_out = (zoom_out or min(dgroup.xdat) >= viewlims[1]
or max(dgroup.xdat) <= viewlims[0]
or min(dgroup.ydat) >= viewlims[3]
or max(dgroup.ydat) <= viewlims[2])
if not zoom_out:
popts['xmin'] = viewlims[0]
popts['xmax'] = viewlims[1]
popts['ymin'] = viewlims[2]
popts['ymax'] = viewlims[3]
popts['xlabel'] = dgroup.plot_xlabel
popts['ylabel'] = dgroup.plot_ylabel
if getattr(dgroup, 'plot_y2label', None) is not None:
popts['y2label'] = dgroup.plot_y2label
plot_choices = PlotSel_Choices
if dgroup.datatype != 'xas':
plot_choices = PlotSel_Choices_nonxas
if multi:
ylabel = self.plotsel_op.GetStringSelection()
yarray_name = plot_choices[ylabel]
if dgroup.datatype == 'xas':
ylabel = getattr(plotlabels, yarray_name, ylabel)
popts['ylabel'] = ylabel
plot_extras = None
if new:
if title is None:
title = fname
plot_extras = getattr(dgroup, 'plot_extras', None)
popts['title'] = title
popts['delay_draw'] = delay_draw
if hasattr(dgroup, 'custom_plotopts'):
popts.update(dgroup.custom_plotopts)
popts['show_legend'] = len(plot_yarrays) > 1
narr = len(plot_yarrays) - 1
for i, pydat in enumerate(plot_yarrays):
yaname, yopts, yalabel = pydat
popts.update(yopts)
if yalabel is not None:
popts['label'] = yalabel
popts['delay_draw'] = delay_draw or (i != narr)
if yaname == 'dnormde' and not hasattr(dgroup, yaname):
self.make_dnormde(dgroup)
if yaname == 'norm_mback' and not hasattr(dgroup, yaname):
self.process(dgroup=dgroup, noskip=True, force_mback=True)
plotcmd(dgroup.xdat, getattr(dgroup, yaname) + yoff, **popts)
plotcmd = ppanel.oplot
if with_extras and plot_extras is not None:
axes = ppanel.axes
for etype, x, y, opts in plot_extras:
if etype == 'marker':
xpopts = {
'marker': 'o',
'markersize': 4,
'label': '_nolegend_',
'markerfacecolor': 'red',
'markeredgecolor': '#884444'
}
xpopts.update(opts)
axes.plot([x], [y], **xpopts)
elif etype == 'vline':
xpopts = {
'ymin': 0,
'ymax': 1.0,
'label': '_nolegend_',
'color': '#888888'
}
xpopts.update(opts)
axes.axvline(x, **xpopts)
if not popts['delay_draw']:
ppanel.canvas.draw()
class XASNormPanel(TaskPanel):
"""XAS normalization Panel"""
def __init__(self, parent, controller=None, **kws):
TaskPanel.__init__(self,
parent,
controller,
configname='xasnorm_config',
config=defaults,
**kws)
def build_display(self):
titleopts = dict(font=Font(12), colour='#AA0000')
xas = self.panel
self.wids = {}
self.plotone_op = Choice(xas,
choices=list(PlotOne_Choices.keys()),
action=self.onPlotOne,
size=(175, -1))
self.plotsel_op = Choice(xas,
choices=list(PlotSel_Choices.keys()),
action=self.onPlotSel,
size=(175, -1))
self.plotone_op.SetSelection(1)
self.plotsel_op.SetSelection(1)
plot_one = Button(xas,
'Plot This Group',
size=(150, -1),
action=self.onPlotOne)
plot_sel = Button(xas,
'Plot Selected Groups',
size=(150, -1),
action=self.onPlotSel)
opts = dict(action=self.onReprocess)
e0opts_panel = wx.Panel(xas)
self.wids['autoe0'] = Check(e0opts_panel,
default=True,
label='auto?',
**opts)
self.wids['showe0'] = Check(e0opts_panel,
default=True,
label='show?',
**opts)
sx = wx.BoxSizer(wx.HORIZONTAL)
sx.Add(self.wids['autoe0'], 0, LCEN, 4)
sx.Add(self.wids['showe0'], 0, LCEN, 4)
pack(e0opts_panel, sx)
self.wids['autostep'] = Check(xas, default=True, label='auto?', **opts)
opts['size'] = (50, -1)
self.wids['vict'] = Choice(xas, choices=('0', '1', '2', '3'), **opts)
self.wids['nnor'] = Choice(xas, choices=('0', '1', '2', '3'), **opts)
self.wids['vict'].SetSelection(1)
self.wids['nnor'].SetSelection(1)
opts.update({'size': (100, -1), 'digits': 2, 'increment': 5.0})
xas_pre1 = self.add_floatspin('pre1', value=-1000, **opts)
xas_pre2 = self.add_floatspin('pre2', value=-30, **opts)
xas_nor1 = self.add_floatspin('nor1', value=50, **opts)
xas_nor2 = self.add_floatspin('nor2', value=5000, **opts)
opts = {'digits': 2, 'increment': 0.1, 'value': 0}
xas_e0 = self.add_floatspin('e0', action=self.onSet_XASE0, **opts)
xas_step = self.add_floatspin('step',
action=self.onSet_XASStep,
with_pin=False,
**opts)
saveconf = Button(xas,
'Save as Default Settings',
size=(200, -1),
action=self.onSaveConfigBtn)
def CopyBtn(name):
return Button(xas,
'Copy',
size=(50, -1),
action=partial(self.onCopyParam, name))
add_text = self.add_text
xas.Add(SimpleText(xas, ' XAS Pre-edge subtraction and Normalization',
**titleopts),
dcol=4)
xas.Add(SimpleText(xas, 'Copy to Selected Groups?'),
style=RCEN,
dcol=3)
xas.Add(plot_sel, newrow=True)
xas.Add(self.plotsel_op, dcol=6)
xas.Add(plot_one, newrow=True)
xas.Add(self.plotone_op, dcol=4)
xas.Add((10, 10))
xas.Add(CopyBtn('plotone_op'), style=RCEN)
add_text('E0 : ')
xas.Add(xas_e0)
xas.Add(e0opts_panel, dcol=3)
xas.Add((10, 1))
xas.Add(CopyBtn('xas_e0'), style=RCEN)
add_text('Edge Step: ')
xas.Add(xas_step)
xas.Add(self.wids['autostep'], dcol=3)
xas.Add((10, 1))
xas.Add(CopyBtn('xas_step'), style=RCEN)
add_text('Pre-edge range: ')
xas.Add(xas_pre1)
add_text(' : ', newrow=False)
xas.Add(xas_pre2)
xas.Add(SimpleText(xas, 'Victoreen:'))
xas.Add(self.wids['vict'])
xas.Add(CopyBtn('xas_pre'), style=RCEN)
add_text('Normalization range: ')
xas.Add(xas_nor1)
add_text(' : ', newrow=False)
xas.Add(xas_nor2)
xas.Add(SimpleText(xas, 'Poly Order:'))
xas.Add(self.wids['nnor'])
xas.Add(CopyBtn('xas_norm'), style=RCEN)
xas.Add(saveconf, dcol=6, newrow=True)
xas.pack()
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add((5, 5), 0, LCEN, 3)
sizer.Add(HLine(self, size=(550, 2)), 0, LCEN, 3)
sizer.Add(xas, 0, LCEN, 3)
sizer.Add((5, 5), 0, LCEN, 3)
sizer.Add(HLine(self, size=(550, 2)), 0, LCEN, 3)
pack(self, sizer)
def get_config(self, dgroup=None):
"""custom get_config to possibly inherit from Athena settings"""
if dgroup is None:
dgroup = self.controller.get_group()
if hasattr(dgroup, self.configname):
conf = getattr(dgroup, self.configname)
else:
conf = self.get_defaultconfig()
if hasattr(dgroup, 'bkg_params'): # from Athena
conf['e0'] = getattr(dgroup.bkg_params, 'e0', conf['e0'])
conf['pre1'] = getattr(dgroup.bkg_params, 'pre1', conf['pre1'])
conf['pre2'] = getattr(dgroup.bkg_params, 'pre2', conf['pre2'])
conf['norm1'] = getattr(dgroup.bkg_params, 'nor1',
conf['norm1'])
conf['norm2'] = getattr(dgroup.bkg_params, 'nor2',
conf['norm2'])
conf['nnorm'] = getattr(dgroup.bkg_params, 'nnor',
conf['nnorm'])
conf['nvict'] = getattr(dgroup.bkg_params, 'nvic',
conf['nvict'])
conf['autostep'] = (float(
getattr(dgroup.bkg_params, 'fixstep', 0.0)) < 0.5)
setattr(dgroup, self.configname, conf)
return conf
def fill_form(self, dgroup):
"""fill in form from a data group"""
opts = self.get_config(dgroup)
self.skip_process = True
if dgroup.datatype == 'xas':
for k in self.wids.values():
k.Enable()
self.plotone_op.SetChoices(list(PlotOne_Choices.keys()))
self.plotsel_op.SetChoices(list(PlotSel_Choices.keys()))
self.plotone_op.SetStringSelection(opts['plotone_op'])
self.plotsel_op.SetStringSelection(opts['plotsel_op'])
self.wids['e0'].SetValue(opts['e0'])
edge_step = opts.get('edge_step', None)
if edge_step is None:
edge_step = 1.0
ndigits = int(2 - round(np.log10(abs(edge_step))))
self.wids['step'].SetDigits(ndigits + 1)
self.wids['step'].SetIncrement(0.2 * 10**(-ndigits))
self.wids['step'].SetValue(edge_step)
self.wids['pre1'].SetValue(opts['pre1'])
self.wids['pre2'].SetValue(opts['pre2'])
self.wids['nor1'].SetValue(opts['norm1'])
self.wids['nor2'].SetValue(opts['norm2'])
self.wids['vict'].SetSelection(opts['nvict'])
self.wids['nnor'].SetSelection(opts['nnorm'])
self.wids['showe0'].SetValue(opts['show_e0'])
self.wids['autoe0'].SetValue(opts['auto_e0'])
self.wids['autostep'].SetValue(opts['auto_step'])
else:
self.plotone_op.SetChoices(list(PlotOne_Choices_nonxas.keys()))
self.plotsel_op.SetChoices(list(PlotSel_Choices_nonxas.keys()))
self.plotone_op.SetStringSelection('Raw Data')
self.plotsel_op.SetStringSelection('Raw Data')
for k in self.wids.values():
k.Disable()
self.skip_process = False
def read_form(self):
"read form, return dict of values"
form_opts = {}
form_opts['e0'] = self.wids['e0'].GetValue()
form_opts['edge_step'] = self.wids['step'].GetValue()
form_opts['pre1'] = self.wids['pre1'].GetValue()
form_opts['pre2'] = self.wids['pre2'].GetValue()
form_opts['norm1'] = self.wids['nor1'].GetValue()
form_opts['norm2'] = self.wids['nor2'].GetValue()
form_opts['nnorm'] = int(self.wids['nnor'].GetSelection())
form_opts['nvict'] = int(self.wids['vict'].GetSelection())
form_opts['plotone_op'] = self.plotone_op.GetStringSelection()
form_opts['plotsel_op'] = self.plotsel_op.GetStringSelection()
form_opts['show_e0'] = self.wids['showe0'].IsChecked()
form_opts['auto_e0'] = self.wids['autoe0'].IsChecked()
form_opts['auto_step'] = self.wids['autostep'].IsChecked()
return form_opts
def onPlotOne(self, evt=None):
self.plot(self.controller.get_group())
def onPlotSel(self, evt=None):
newplot = True
group_ids = self.controller.filelist.GetCheckedStrings()
if len(group_ids) < 1:
return
last_id = group_ids[-1]
yarray_name = PlotSel_Choices[self.plotsel_op.GetStringSelection()]
ylabel = getattr(plotlabels, yarray_name)
for checked in group_ids:
groupname = self.controller.file_groups[str(checked)]
dgroup = self.controller.get_group(groupname)
plot_yarrays = [(yarray_name, PLOTOPTS_1, dgroup.filename)]
if dgroup is not None:
dgroup.plot_extras = []
self.plot(dgroup,
title='',
new=newplot,
multi=True,
plot_yarrays=plot_yarrays,
show_legend=True,
with_extras=False,
delay_draw=(last_id != checked))
newplot = False
self.controller.get_display(stacked=False).panel.canvas.draw()
def onSaveConfigBtn(self, evt=None):
conf = self.get_config()
conf.update(self.read_form())
self.set_defaultconfig(conf)
def onCopyParam(self, name=None, evt=None):
conf = self.get_config()
conf.update(self.read_form())
opts = {}
name = str(name)
def copy_attrs(*args):
for a in args:
opts[a] = conf[a]
if name == 'plotone_op':
copy_attrs('plotone_op')
elif name == 'xas_e0':
copy_attrs('e0', 'show_e0', 'auto_e0')
elif name == 'xas_step':
copy_attrs('edge_step', 'auto_step')
elif name == 'xas_pre':
copy_attrs('pre1', 'pre2', 'nvict')
elif name == 'xas_norm':
copy_attrs('nnorm', 'norm1', 'norm2')
for checked in self.controller.filelist.GetCheckedStrings():
groupname = self.controller.file_groups[str(checked)]
grp = self.controller.get_group(groupname)
if grp != self.controller.group:
self.set_config(grp, opts)
self.fill_form(grp)
self.process(grp)
def onSet_XASE0(self, evt=None, value=None):
"handle setting e0"
self.wids['autoe0'].SetValue(0)
self.onReprocess()
def onSet_XASStep(self, evt=None, value=None):
"handle setting edge step"
self.wids['autostep'].SetValue(0)
self.onReprocess()
def onSelPoint(self, evt=None, opt='__', win=None):
"""
get last selected point from a specified plot window
and fill in the value for the widget defined by `opt`.
by default it finds the latest cursor position from the
cursor history of the first 20 plot windows.
"""
if opt not in self.wids:
return None
_x, _y = last_cursor_pos(win=win, _larch=self.larch)
if _x is None:
return
e0 = self.wids['e0'].GetValue()
if opt == 'e0':
self.wids['e0'].SetValue(_x)
self.wids['autoe0'].SetValue(0)
elif opt in ('pre1', 'pre2', 'nor1', 'nor2'):
self.wids[opt].SetValue(_x - e0)
self.onReprocess()
def onReprocess(self, evt=None, value=None, **kws):
"handle request reprocess"
if self.skip_process:
return
try:
dgroup = self.controller.get_group()
except TypeError:
return
self.process(dgroup=dgroup)
self.plot(dgroup)
def make_dnormde(self, dgroup):
form = dict(group=dgroup.groupname)
self.larch_eval(
"{group:s}.dnormde={group:s}.dmude/{group:s}.edge_step".format(
**form))
def process(self, dgroup=None, **kws):
""" handle process (pre-edge/normalize) of XAS data from XAS form
"""
if self.skip_process:
return
if dgroup is None:
dgroup = self.controller.get_group()
self.skip_process = True
# print("process ", dgroup, dgroup.filename)
self.get_config(dgroup)
dgroup.custom_plotopts = {}
# print("XAS norm process ", dgroup.datatype)
if dgroup.datatype != 'xas':
self.skip_process = False
dgroup.mu = dgroup.ydat * 1.0
return
en_units = getattr(dgroup, 'energy_units', None)
if en_units is None:
en_units = 'eV'
units = guess_energy_units(dgroup.energy)
if units != 'eV':
dlg = EnergyUnitsDialog(self.parent, units, dgroup.energy)
res = dlg.GetResponse()
dlg.Destroy()
if res.ok:
en_units = res.units
dgroup.xdat = dgroup.energy = res.energy
dgroup.energy_units = en_units
form = self.read_form()
e0 = form['e0']
edge_step = form['edge_step']
form['group'] = dgroup.groupname
copts = [dgroup.groupname]
if not form['auto_e0']:
if e0 < max(dgroup.energy) and e0 > min(dgroup.energy):
copts.append("e0=%.4f" % float(e0))
if not form['auto_step']:
copts.append("step=%.4f" % float(edge_step))
for attr in ('pre1', 'pre2', 'nvict', 'nnorm', 'norm1', 'norm2'):
copts.append("%s=%.2f" % (attr, form[attr]))
self.larch_eval("pre_edge(%s)" % (', '.join(copts)))
self.make_dnormde(dgroup)
if form['auto_e0']:
self.wids['e0'].SetValue(dgroup.e0) # , act=False)
if form['auto_step']:
self.wids['step'].SetValue(dgroup.edge_step) # , act=False)
self.wids['pre1'].SetValue(dgroup.pre_edge_details.pre1)
self.wids['pre2'].SetValue(dgroup.pre_edge_details.pre2)
self.wids['nor1'].SetValue(dgroup.pre_edge_details.norm1)
self.wids['nor2'].SetValue(dgroup.pre_edge_details.norm2)
conf = {}
for attr in ('e0', 'edge_step'):
conf[attr] = getattr(dgroup, attr)
for attr in ('pre1', 'pre2', 'nnorm', 'norm1', 'norm2'):
conf[attr] = getattr(dgroup.pre_edge_details, attr)
self.set_config(dgroup, conf)
self.skip_process = False
def get_plot_arrays(self, dgroup):
form = self.read_form()
lab = plotlabels.norm
if dgroup is None:
return
dgroup.plot_y2label = None
dgroup.plot_xlabel = plotlabels.energy
dgroup.plot_yarrays = [('norm', PLOTOPTS_1, lab)]
if dgroup.datatype != 'xas':
pchoice = PlotOne_Choices_nonxas[
self.plotone_op.GetStringSelection()]
dgroup.plot_xlabel = 'x'
dgroup.plot_ylabel = 'y'
dgroup.plot_yarrays = [('ydat', PLOTOPTS_1, 'ydat')]
dgroup.dmude = np.gradient(dgroup.ydat) / np.gradient(dgroup.xdat)
if pchoice == 'dmude':
dgroup.plot_ylabel = 'dy/dx'
dgroup.plot_yarrays = [('dmude', PLOTOPTS_1, 'dy/dx')]
elif pchoice == 'norm+deriv':
lab = plotlabels.norm
dgroup.plot_y2label = 'dy/dx'
dgroup.plot_yarrays = [('ydat', PLOTOPTS_1, 'y'),
('dmude', PLOTOPTS_D, 'dy/dx')]
return
pchoice = PlotOne_Choices[self.plotone_op.GetStringSelection()]
if pchoice in ('mu', 'norm', 'flat', 'dmude'):
lab = getattr(plotlabels, pchoice)
dgroup.plot_yarrays = [(pchoice, PLOTOPTS_1, lab)]
elif pchoice == 'prelines':
dgroup.plot_yarrays = [('mu', PLOTOPTS_1, plotlabels.mu),
('pre_edge', PLOTOPTS_2, 'pre edge'),
('post_edge', PLOTOPTS_2, 'post edge')]
elif pchoice == 'preedge':
dgroup.pre_edge_sub = dgroup.norm * dgroup.edge_step
dgroup.plot_yarrays = [('pre_edge_sub', PLOTOPTS_1,
r'pre-edge subtracted $\mu$')]
lab = r'pre-edge subtracted $\mu$'
elif pchoice == 'norm+deriv':
lab = plotlabels.norm
lab2 = plotlabels.dmude
dgroup.plot_yarrays = [('norm', PLOTOPTS_1, lab),
('dmude', PLOTOPTS_D, lab2)]
dgroup.plot_y2label = lab2
dgroup.plot_ylabel = lab
y4e0 = dgroup.ydat = getattr(dgroup, dgroup.plot_yarrays[0][0],
dgroup.mu)
dgroup.plot_extras = []
if form['show_e0']:
ie0 = index_of(dgroup.energy, dgroup.e0)
dgroup.plot_extras.append(('marker', dgroup.e0, y4e0[ie0], {}))
def plot(self,
dgroup,
title=None,
plot_yarrays=None,
delay_draw=False,
multi=False,
new=True,
zoom_out=True,
with_extras=True,
**kws):
self.get_plot_arrays(dgroup)
ppanel = self.controller.get_display(stacked=False).panel
viewlims = ppanel.get_viewlimits()
plotcmd = ppanel.oplot
if new:
plotcmd = ppanel.plot
groupname = dgroup.groupname
if not hasattr(dgroup, 'xdat'):
print("Cannot plot group ", groupname)
if ((getattr(dgroup, 'plot_yarrays', None) is None
or getattr(dgroup, 'energy', None) is None
or getattr(dgroup, 'mu', None) is None)):
self.process(dgroup=dgroup)
if plot_yarrays is None and hasattr(dgroup, 'plot_yarrays'):
plot_yarrays = dgroup.plot_yarrays
popts = kws
path, fname = os.path.split(dgroup.filename)
if 'label' not in popts:
popts['label'] = dgroup.plot_ylabel
zoom_out = (zoom_out or min(dgroup.xdat) >= viewlims[1]
or max(dgroup.xdat) <= viewlims[0]
or min(dgroup.ydat) >= viewlims[3]
or max(dgroup.ydat) <= viewlims[2])
if not zoom_out:
popts['xmin'] = viewlims[0]
popts['xmax'] = viewlims[1]
popts['ymin'] = viewlims[2]
popts['ymax'] = viewlims[3]
popts['xlabel'] = dgroup.plot_xlabel
popts['ylabel'] = dgroup.plot_ylabel
if getattr(dgroup, 'plot_y2label', None) is not None:
popts['y2label'] = dgroup.plot_y2label
if multi:
yarray_name = PlotSel_Choices[self.plotsel_op.GetStringSelection()]
popts['ylabel'] = getattr(plotlabels, yarray_name)
plot_extras = None
if new:
if title is None:
title = fname
plot_extras = getattr(dgroup, 'plot_extras', None)
popts['title'] = title
popts['delay_draw'] = delay_draw
if hasattr(dgroup, 'custom_plotopts'):
popts.update(dgroup.custom_plotopts)
narr = len(plot_yarrays) - 1
for i, pydat in enumerate(plot_yarrays):
yaname, yopts, yalabel = pydat
popts.update(yopts)
if yalabel is not None:
popts['label'] = yalabel
popts['delay_draw'] = delay_draw or (i != narr)
# print("plot:: ", i, popts['delay_draw'], plotcmd, popts)
if yaname == 'dnormde' and not hasattr(dgroup, yaname):
self.make_dnormde(dgroup)
plotcmd(dgroup.xdat, getattr(dgroup, yaname), **popts)
plotcmd = ppanel.oplot
if with_extras and plot_extras is not None:
axes = ppanel.axes
for etype, x, y, opts in plot_extras:
if etype == 'marker':
xpopts = {
'marker': 'o',
'markersize': 4,
'label': '_nolegend_',
'markerfacecolor': 'red',
'markeredgecolor': '#884444'
}
xpopts.update(opts)
axes.plot([x], [y], **xpopts)
elif etype == 'vline':
xpopts = {
'ymin': 0,
'ymax': 1.0,
'label': '_nolegend_',
'color': '#888888'
}
xpopts.update(opts)
axes.axvline(x, **xpopts)
if not popts['delay_draw']:
ppanel.canvas.draw()