class XASNormPanel(wx.Panel):
"""XAS normalization Panel"""
def __init__(self, parent, controller=None, reporter=None, **kws):
wx.Panel.__init__(self, parent, -1, **kws)
self.parent = parent
self.controller = controller
self.reporter = reporter
self.skip_process = False
self.build_display()
def onPanelExposed(self, **kws):
# called when notebook is selected
try:
fname = self.controller.filelist.GetStringSelection()
gname = self.controller.file_groups[fname]
dgroup = self.controller.get_group(gname)
self.fill_form(dgroup)
except:
pass
def larch_eval(self, cmd):
"""eval"""
self.controller.larch.eval(cmd)
def build_display(self):
self.SetFont(Font(10))
titleopts = dict(font=Font(11), colour='#AA0000')
xas = self.xaspanel = GridPanel(self,
ncols=4,
nrows=4,
pad=2,
itemstyle=LCEN)
self.plotone_op = Choice(xas,
choices=list(PlotOne_Choices.keys()),
action=self.onPlotOne,
size=(200, -1))
self.plotsel_op = Choice(xas,
choices=list(PlotSel_Choices.keys()),
action=self.onPlotSel,
size=(200, -1))
self.plotone_op.SetStringSelection('Normalized')
self.plotsel_op.SetStringSelection('Normalized')
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)
self.btns = {}
opts = dict(action=self.onReprocess)
self.deconv_ewid = FloatCtrl(xas,
value=0.5,
precision=2,
minval=0,
size=(50, -1),
**opts)
self.deconv_form = Choice(xas,
choices=DECONV_OPS,
size=(100, -1),
**opts)
e0opts_panel = wx.Panel(xas)
self.xas_autoe0 = Check(e0opts_panel,
default=True,
label='auto?',
**opts)
self.xas_showe0 = Check(e0opts_panel,
default=True,
label='show?',
**opts)
sx = wx.BoxSizer(wx.HORIZONTAL)
sx.Add(self.xas_autoe0, 0, LCEN, 4)
sx.Add(self.xas_showe0, 0, LCEN, 4)
pack(e0opts_panel, sx)
self.xas_autostep = Check(xas, default=True, label='auto?', **opts)
for name in ('e0', 'pre1', 'pre2', 'nor1', 'nor2'):
bb = BitmapButton(xas,
get_icon('plus'),
action=partial(self.on_selpoint, opt=name),
tooltip='use last point selected from plot')
self.btns[name] = bb
opts['size'] = (50, -1)
self.xas_vict = Choice(xas, choices=('0', '1', '2', '3'), **opts)
self.xas_nnor = Choice(xas, choices=('0', '1', '2', '3'), **opts)
self.xas_vict.SetSelection(1)
self.xas_nnor.SetSelection(1)
opts.update({'size': (75, -1), 'precision': 1})
self.xas_pre1 = FloatCtrl(xas, value=-np.inf, **opts)
self.xas_pre2 = FloatCtrl(xas, value=-30, **opts)
self.xas_nor1 = FloatCtrl(xas, value=50, **opts)
self.xas_nor2 = FloatCtrl(xas, value=np.inf, **opts)
opts = {'size': (75, -1), 'gformat': True}
self.xas_e0 = FloatCtrl(xas, value=0, action=self.onSet_XASE0, **opts)
self.xas_step = FloatCtrl(xas,
value=0,
action=self.onSet_XASStep,
**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))
xas.Add(SimpleText(xas, ' XAS Pre-edge subtraction and Normalization',
**titleopts),
dcol=6)
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=6)
xas.Add((10, 10))
xas.Add(CopyBtn('plotone_op'), style=RCEN)
xas.Add(SimpleText(xas, 'E0 : '), newrow=True)
xas.Add(self.btns['e0'])
xas.Add(self.xas_e0)
xas.Add(e0opts_panel, dcol=4)
xas.Add((10, 1))
xas.Add(CopyBtn('xas_e0'), style=RCEN)
xas.Add(SimpleText(xas, 'Edge Step: '), newrow=True)
xas.Add((10, 1))
xas.Add(self.xas_step)
xas.Add(self.xas_autostep, dcol=3)
xas.Add((10, 1))
xas.Add((10, 1))
xas.Add(CopyBtn('xas_step'), style=RCEN)
xas.Add(SimpleText(xas, 'Pre-edge range: '), newrow=True)
xas.Add(self.btns['pre1'])
xas.Add(self.xas_pre1)
xas.Add(SimpleText(xas, ':'))
xas.Add(self.btns['pre2'])
xas.Add(self.xas_pre2)
xas.Add(SimpleText(xas, 'Victoreen:'))
xas.Add(self.xas_vict)
xas.Add(CopyBtn('xas_pre'), style=RCEN)
xas.Add(SimpleText(xas, 'Normalization range: '), newrow=True)
xas.Add(self.btns['nor1'])
xas.Add(self.xas_nor1)
xas.Add(SimpleText(xas, ':'))
xas.Add(self.btns['nor2'])
xas.Add(self.xas_nor2)
xas.Add(SimpleText(xas, 'Poly Order:'))
xas.Add(self.xas_nnor)
xas.Add(CopyBtn('xas_norm'), style=RCEN)
xas.Add(SimpleText(xas, ' Deconvolution:'), newrow=True)
xas.Add(self.deconv_form, dcol=5)
xas.Add(SimpleText(xas, 'Energy width:'))
xas.Add(self.deconv_ewid)
xas.Add(CopyBtn('deconv'), 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):
"""get processing configuration for a group"""
if dgroup is None:
dgroup = self.controller.get_group()
conf = getattr(dgroup, 'xasnorm_config', {})
if 'e0' not in conf:
conf = default_xasnorm_config()
dgroup.xasnorm_config = conf
return conf
def fill_form(self, dgroup):
"""fill in form from a data group"""
opts = self.get_config(dgroup)
self.skip_process = True
widlist = (self.xas_e0, self.xas_step, self.xas_pre1, self.xas_pre2,
self.xas_nor1, self.xas_nor2, self.xas_vict, self.xas_nnor,
self.xas_showe0, self.xas_autoe0, self.xas_autostep,
self.deconv_form, self.deconv_ewid)
if dgroup.datatype == 'xas':
for k in widlist:
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.xas_e0.SetValue(opts['e0'])
self.xas_step.SetValue(opts['edge_step'])
self.xas_pre1.SetValue(opts['pre1'])
self.xas_pre2.SetValue(opts['pre2'])
self.xas_nor1.SetValue(opts['norm1'])
self.xas_nor2.SetValue(opts['norm2'])
self.xas_vict.SetSelection(opts['nvict'])
self.xas_nnor.SetSelection(opts['nnorm'])
self.xas_showe0.SetValue(opts['show_e0'])
self.xas_autoe0.SetValue(opts['auto_e0'])
self.xas_autostep.SetValue(opts['auto_step'])
self.deconv_form.SetStringSelection(opts['deconv_form'])
self.deconv_ewid.SetValue(opts['deconv_ewid'])
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 widlist:
k.Disable()
self.skip_process = False
self.process(dgroup)
def read_form(self):
"read for, returning dict of values"
form_opts = {}
form_opts['e0'] = self.xas_e0.GetValue()
form_opts['edge_step'] = self.xas_step.GetValue()
form_opts['pre1'] = self.xas_pre1.GetValue()
form_opts['pre2'] = self.xas_pre2.GetValue()
form_opts['norm1'] = self.xas_nor1.GetValue()
form_opts['norm2'] = self.xas_nor2.GetValue()
form_opts['nnorm'] = int(self.xas_nnor.GetSelection())
form_opts['nvict'] = int(self.xas_vict.GetSelection())
form_opts['plotone_op'] = self.plotone_op.GetStringSelection()
form_opts['plotsel_op'] = self.plotsel_op.GetStringSelection()
form_opts['show_e0'] = self.xas_showe0.IsChecked()
form_opts['auto_e0'] = self.xas_autoe0.IsChecked()
form_opts['auto_step'] = self.xas_autostep.IsChecked()
form_opts['deconv_form'] = self.deconv_form.GetStringSelection()
form_opts['deconv_ewid'] = self.deconv_ewid.GetValue()
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)
# print("Plot Sel:: ", group_ids)
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)]
dgroup.plot_ylabel = ylabel
if dgroup is not None:
dgroup.plot_extras = []
# print(" PlotSel -> plot ", checked, (last_id!=checked) )
self.plot(dgroup,
title='',
new=newplot,
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.controller.larch.symtable._sys.xas_viewer
opts = {}
opts.update(getattr(conf, 'xas_norm', {}))
opts.update(self.read_form())
conf.xas_norm = opts
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')
opts['auto_e0'] = False
elif name == 'xas_step':
copy_attrs('edge_step')
opts['auto_step'] = False
elif name == 'xas_pre':
copy_attrs('pre1', 'pre2', 'nvict')
elif name == 'xas_norm':
copy_attrs('nnorm', 'norm1', 'norm2')
elif name == 'deconv':
copy_attrs('deconv_form', 'deconv_ewid')
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:
grp.xasnorm_config.update(opts)
self.fill_form(grp)
self.process(grp)
def onSet_XASE0(self, evt=None, value=None):
self.xas_autoe0.SetValue(0)
self.onReprocess()
def onSet_XASStep(self, evt=None, value=None):
self.xas_autostep.SetValue(0)
self.onReprocess()
def onReprocess(self, evt=None, value=None, **kws):
if self.skip_process:
return
try:
dgroup = self.controller.get_group()
except TypeError:
return
self.process(dgroup)
self.plot(dgroup)
def on_selpoint(self, evt=None, opt='e0'):
xval, yval = self.controller.get_cursor()
if xval is None:
return
e0 = self.xas_e0.GetValue()
if opt == 'e0':
self.xas_e0.SetValue(xval)
self.xas_autoe0.SetValue(0)
elif opt == 'pre1':
self.xas_pre1.SetValue(xval - e0)
elif opt == 'pre2':
self.xas_pre2.SetValue(xval - e0)
elif opt == 'nor1':
self.xas_nor1.SetValue(xval - e0)
elif opt == 'nor2':
self.xas_nor2.SetValue(xval - e0)
else:
print(" unknown selection point ", opt)
def process(self, dgroup, **kws):
""" handle process (pre-edge/normalize, deconvolve) of XAS data from XAS form
"""
if self.skip_process:
return
self.skip_process = True
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)))
if form['auto_e0']:
self.xas_e0.SetValue(dgroup.e0, act=False)
if form['auto_step']:
self.xas_step.SetValue(dgroup.edge_step, act=False)
self.xas_pre1.SetValue(dgroup.pre_edge_details.pre1)
self.xas_pre2.SetValue(dgroup.pre_edge_details.pre2)
self.xas_nor1.SetValue(dgroup.pre_edge_details.norm1)
self.xas_nor2.SetValue(dgroup.pre_edge_details.norm2)
# deconvolution
deconv_form = form['deconv_form'].lower()
deconv_ewid = float(form['deconv_ewid'])
if not deconv_form.startswith('none') and deconv_ewid > 1.e-3:
dopts = [
dgroup.groupname,
"form='%s'" % (deconv_form),
"esigma=%.4f" % (deconv_ewid)
]
self.larch_eval("xas_deconvolve(%s)" % (', '.join(dopts)))
for attr in ('e0', 'edge_step'):
dgroup.xasnorm_config[attr] = getattr(dgroup, attr)
for attr in ('pre1', 'pre2', 'nnorm', 'norm1', 'norm2'):
dgroup.xasnorm_config[attr] = getattr(dgroup.pre_edge_details,
attr)
self.skip_process = False
def get_plot_arrays(self, dgroup):
form = self.read_form()
lab = plotlabels.norm
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, lab),
('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
elif pchoice == 'deconv' and hasattr(dgroup, 'deconv'):
lab = plotlabels.deconv
dgroup.plot_yarrays = [('deconv', PLOTOPTS_1, lab)]
elif pchoice == 'deconv+norm' and hasattr(dgroup, 'deconv'):
lab1 = plotlabels.norm
lab2 = plotlabels.deconv
dgroup.plot_yarrays = [('deconv', PLOTOPTS_1, lab2),
('norm', PLOTOPTS_1, lab1)]
lab = lab1 + ' + ' + 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,
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)
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 not 'label' 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_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)
# print(popts)
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()
class XYFitPanel(wx.Panel):
def __init__(self, parent=None, controller=None, **kws):
wx.Panel.__init__(self, parent, -1, size=(550, 500), **kws)
self.parent = parent
self.controller = controller
self.larch = controller.larch
self.fit_components = OrderedDict()
self.fit_model = None
self.fit_params = None
self.user_added_params = None
self.summary = None
self.sizer = wx.GridBagSizer(10, 6)
self.build_display()
self.pick2_timer = wx.Timer(self)
self.pick2_group = None
self.Bind(wx.EVT_TIMER, self.onPick2Timer, self.pick2_timer)
self.pick2_t0 = 0.
self.pick2_timeout = 15.
self.pick2erase_timer = wx.Timer(self)
self.pick2erase_panel = None
self.Bind(wx.EVT_TIMER, self.onPick2EraseTimer, self.pick2erase_timer)
def build_display(self):
self.mod_nb = flat_nb.FlatNotebook(self, -1, agwStyle=FNB_STYLE)
self.mod_nb.SetTabAreaColour(wx.Colour(250, 250, 250))
self.mod_nb.SetActiveTabColour(wx.Colour(254, 254, 195))
self.mod_nb.SetNonActiveTabTextColour(wx.Colour(10, 10, 128))
self.mod_nb.SetActiveTabTextColour(wx.Colour(128, 0, 0))
self.mod_nb.Bind(wx.EVT_NOTEBOOK_PAGE_CHANGED, self.onNBChanged)
self.param_panel = AllParamsPanel(self, controller=self.controller)
# self.mod_nb.AddPage(self.param_panel, 'Parameters', True)
range_row = wx.Panel(self)
rsizer = wx.BoxSizer(wx.HORIZONTAL)
xmin_sel = BitmapButton(range_row,
get_icon('plus'),
action=partial(self.on_selpoint, opt='xmin'),
tooltip='use last point selected from plot')
xmax_sel = BitmapButton(range_row,
get_icon('plus'),
action=partial(self.on_selpoint, opt='xmax'),
tooltip='use last point selected from plot')
opts = {'size': (70, -1), 'gformat': True}
self.xmin = FloatCtrl(range_row, value=-np.inf, **opts)
self.xmax = FloatCtrl(range_row, value=np.inf, **opts)
rsizer.Add(SimpleText(range_row, 'Fit Range X=[ '), 0, LCEN, 3)
rsizer.Add(xmin_sel, 0, LCEN, 3)
rsizer.Add(self.xmin, 0, LCEN, 3)
rsizer.Add(SimpleText(range_row, ' : '), 0, LCEN, 3)
rsizer.Add(xmax_sel, 0, LCEN, 3)
rsizer.Add(self.xmax, 0, LCEN, 3)
rsizer.Add(SimpleText(range_row, ' ] '), 0, LCEN, 3)
rsizer.Add(
Button(range_row,
'Full Data Range',
size=(150, -1),
action=self.onResetRange), 0, LCEN, 3)
pack(range_row, rsizer)
action_row = wx.Panel(self)
rsizer = wx.BoxSizer(wx.HORIZONTAL)
self.plot_comps = Check(action_row,
label='Plot Components?',
default=True,
size=(150, -1))
rsizer.Add(
Button(action_row, 'Run Fit', size=(100, -1),
action=self.onRunFit), 0, RCEN, 3)
savebtn = Button(action_row,
'Save Fit',
size=(100, -1),
action=self.onSaveFit)
savebtn.Disable()
rsizer.Add(savebtn, 0, LCEN, 3)
rsizer.Add(
Button(action_row,
'Plot Current Model',
size=(150, -1),
action=self.onShowModel), 0, LCEN, 3)
rsizer.Add(self.plot_comps, 0, LCEN, 3)
pack(action_row, rsizer)
models_row = wx.Panel(self)
rsizer = wx.BoxSizer(wx.HORIZONTAL)
self.model_choice = Choice(models_row,
size=(200, -1),
choices=ModelChoices['peaks'],
action=self.addModel)
rsizer.Add(SimpleText(models_row, ' Add Model Type: '), 0, LCEN, 3)
rsizer.Add(
Choice(models_row,
size=(100, -1),
choices=ModelTypes,
action=self.onModelTypes), 0, LCEN, 3)
rsizer.Add(SimpleText(models_row, ' Model: '), 0, LCEN, 3)
rsizer.Add(self.model_choice, 0, LCEN, 3)
pack(models_row, rsizer)
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.AddMany([(range_row, 0, LCEN, 4), ((9, 9), 0, LCEN, 4),
(models_row, 0, LCEN, 4), ((9, 9), 0, LCEN, 4),
(action_row, 0, LCEN, 4), ((9, 9), 0, LCEN, 4),
(HLine(self, size=(550, 3)), 0, LCEN, 4),
((10, 10), 0, LCEN, 2),
(self.mod_nb, 1, LCEN | wx.GROW, 10)])
pack(self, sizer)
def onNBChanged(self, event=None):
idx = self.mod_nb.GetSelection()
if self.mod_nb.GetPage(idx) is self.param_panel:
self.build_fitmodel()
self.param_panel.show_parameters(self.fit_params,
self.user_added_params)
def onModelTypes(self, event=None):
modtype = event.GetString().lower()
self.model_choice.SetChoices(ModelChoices[modtype])
def addModel(self, event=None, model=None):
if model is None and event is not None:
model = event.GetString()
if model is None or model.startswith('<'):
return
curmodels = [
"c%i_" % (i + 1) for i in range(1 + len(self.fit_components))
]
for comp in self.fit_components:
if comp in curmodels:
curmodels.remove(comp)
prefix = curmodels[0]
label = "%s(prefix='%s')" % (model, prefix)
title = "%s: %s" % (prefix[:-1], (model + ' ' * 8)[:8])
mclass_kws = {'prefix': prefix}
if 'step' in model.lower():
form = model.lower().replace('step', '').strip()
if form.startswith('err'): form = 'erf'
label = "Step(form='%s', prefix='%s')" % (form, prefix)
title = "%s: Step %s" % (prefix[:-1], form[:3])
mclass = lm_models.StepModel
mclass_kws['form'] = form
minst = mclass(form=form, prefix=prefix)
else:
mclass = getattr(lm_models, model + 'Model')
minst = mclass(prefix=prefix)
panel = GridPanel(self.mod_nb, ncols=1, nrows=1, pad=1, itemstyle=CEN)
def SLabel(label, size=(80, -1), **kws):
return SimpleText(panel,
label,
size=size,
style=wx.ALIGN_LEFT,
**kws)
usebox = Check(panel, default=True, label='Use?', size=(75, -1))
delbtn = Button(panel,
'Delete Model',
size=(120, -1),
action=partial(self.onDeleteComponent, prefix=prefix))
pick2msg = SimpleText(panel, " ", size=(75, -1))
pick2btn = Button(panel,
'Pick Data Range',
size=(135, -1),
action=partial(self.onPick2Points, prefix=prefix))
# SetTip(mname, 'Label for the model component')
SetTip(usebox, 'Use this component in fit?')
SetTip(delbtn, 'Delete this model component')
SetTip(pick2btn, 'Select X range on Plot to Guess Initial Values')
panel.Add(HLine(panel, size=(520, 3)), style=wx.ALIGN_CENTER, dcol=6)
panel.Add(SLabel(label, size=(200, -1), colour='#0000AA'),
dcol=3,
newrow=True)
panel.AddMany((usebox, pick2msg, pick2btn))
panel.Add(SLabel("Parameter"), newrow=True)
panel.AddMany((SLabel("Value"), SLabel("Type"), SLabel("Min"),
SLabel("Max"), SLabel("Expression")))
parwids = OrderedDict()
parnames = sorted(minst.param_names)
for a in minst._func_allargs:
pname = "%s%s" % (prefix, a)
if (pname not in parnames and a in minst.param_hints
and a not in minst.independent_vars):
parnames.append(pname)
for pname in parnames:
sname = pname[len(prefix):]
hints = minst.param_hints.get(sname, {})
par = Parameter(name=pname, value=0, vary=True)
if 'min' in hints:
par.min = hints['min']
if 'max' in hints:
par.max = hints['max']
if 'value' in hints:
par.value = hints['value']
if 'expr' in hints:
par.expr = hints['expr']
pwids = ParameterWidgets(panel,
par,
name_size=80,
expr_size=175,
float_size=80,
prefix=prefix,
widgets=('name', 'value', 'minval',
'maxval', 'vary', 'expr'))
parwids[par.name] = pwids
panel.Add(pwids.name, newrow=True)
panel.AddMany((pwids.value, pwids.vary, pwids.minval, pwids.maxval,
pwids.expr))
for sname, hint in minst.param_hints.items():
pname = "%s%s" % (prefix, sname)
if 'expr' in hint and pname not in parnames:
par = Parameter(name=pname, value=0, expr=hint['expr'])
pwids = ParameterWidgets(panel,
par,
name_size=80,
expr_size=275,
float_size=80,
prefix=prefix,
widgets=('name', 'value', 'vary',
'expr'))
parwids[par.name] = pwids
panel.Add(pwids.name, newrow=True)
panel.AddMany((pwids.value, pwids.vary))
panel.Add(pwids.expr, dcol=3, style=wx.ALIGN_RIGHT)
pwids.value.Disable()
pwids.vary.Disable()
panel.Add(HLine(panel, size=(90, 3)),
style=wx.ALIGN_CENTER,
newrow=True)
panel.Add(delbtn, dcol=2)
panel.Add(HLine(panel, size=(250, 3)), dcol=3, style=wx.ALIGN_CENTER)
fgroup = Group(prefix=prefix,
title=title,
mclass=mclass,
mclass_kws=mclass_kws,
usebox=usebox,
panel=panel,
parwids=parwids,
float_size=65,
expr_size=150,
pick2_msg=pick2msg)
self.fit_components[prefix] = fgroup
panel.pack()
self.mod_nb.AddPage(panel, title, True)
sx, sy = self.GetSize()
self.SetSize((sx, sy + 1))
self.SetSize((sx, sy))
def onDeleteComponent(self, evt=None, prefix=None):
fgroup = self.fit_components.get(prefix, None)
if fgroup is None:
return
for i in range(self.mod_nb.GetPageCount()):
if fgroup.title == self.mod_nb.GetPageText(i):
self.mod_nb.DeletePage(i)
for attr in dir(fgroup):
setattr(fgroup, attr, None)
self.fit_components.pop(prefix)
sx, sy = self.GetSize()
self.SetSize((sx, sy + 1))
self.SetSize((sx, sy))
def onPick2EraseTimer(self, evt=None):
"""erases line trace showing automated 'Pick 2' guess """
self.pick2erase_timer.Stop()
panel = self.pick2erase_panel
ntrace = panel.conf.ntrace - 1
trace = panel.conf.get_mpl_line(ntrace)
panel.conf.get_mpl_line(ntrace).set_data(np.array([]), np.array([]))
panel.conf.ntrace = ntrace
panel.draw()
def onPick2Timer(self, evt=None):
"""checks for 'Pick 2' events, and initiates 'Pick 2' guess
for a model from the selected data range
"""
try:
plotframe = self.controller.get_display(stacked=False)
curhist = plotframe.cursor_hist[:]
plotframe.Raise()
except:
return
if (time.time() - self.pick2_t0) > self.pick2_timeout:
msg = self.pick2_group.pick2_msg.SetLabel(" ")
plotframe.cursor_hist = []
self.pick2_timer.Stop()
return
if len(curhist) < 2:
self.pick2_group.pick2_msg.SetLabel("%i/2" % (len(curhist)))
return
self.pick2_group.pick2_msg.SetLabel("done.")
self.pick2_timer.Stop()
# guess param values
xcur = (curhist[0][0], curhist[1][0])
xmin, xmax = min(xcur), max(xcur)
dgroup = getattr(self.larch.symtable, self.controller.groupname)
x, y = dgroup.x, dgroup.y
i0 = index_of(dgroup.x, xmin)
i1 = index_of(dgroup.x, xmax)
x, y = dgroup.x[i0:i1 + 1], dgroup.y[i0:i1 + 1]
mod = self.pick2_group.mclass(prefix=self.pick2_group.prefix)
parwids = self.pick2_group.parwids
try:
guesses = mod.guess(y, x=x)
except:
return
for name, param in guesses.items():
if name in parwids:
parwids[name].value.SetValue(param.value)
dgroup._tmp = mod.eval(guesses, x=dgroup.x)
plotframe = self.controller.get_display(stacked=False)
plotframe.cursor_hist = []
plotframe.oplot(dgroup.x, dgroup._tmp)
self.pick2erase_panel = plotframe.panel
self.pick2erase_timer.Start(5000)
def onPick2Points(self, evt=None, prefix=None):
fgroup = self.fit_components.get(prefix, None)
if fgroup is None:
return
plotframe = self.controller.get_display(stacked=False)
plotframe.Raise()
plotframe.cursor_hist = []
fgroup.npts = 0
self.pick2_group = fgroup
if fgroup.pick2_msg is not None:
fgroup.pick2_msg.SetLabel("0/2")
self.pick2_t0 = time.time()
self.pick2_timer.Start(250)
def onSaveFit(self, event=None):
dgroup = self.get_datagroup()
deffile = dgroup.filename.replace('.', '_') + '.fitconf'
outfile = FileSave(self,
'Save Fit Configuration and Results',
default_file=deffile,
wildcard=FITCONF_WILDCARDS)
if outfile is None:
return
buff = ['#XYFit Config version 1']
buff.append(
json.dumps(encode4js(self.summary), encoding='UTF-8', default=str))
buff.append('')
try:
fout = open(outfile, 'w')
fout.write('\n'.join(buff))
fout.close()
except IOError:
print('could not write %s' % outfile)
def onResetRange(self, event=None):
dgroup = self.get_datagroup()
self.xmin.SetValue(min(dgroup.x))
self.xmax.SetValue(max(dgroup.x))
def on_selpoint(self, evt=None, opt='xmin'):
xval = None
try:
xval = self.larch.symtable._plotter.plot1_x
except:
xval = None
if xval is not None:
if opt == 'xmin':
self.xmin.SetValue(xval)
elif opt == 'xmax':
self.xmax.SetValue(xval)
def get_datagroup(self):
dgroup = None
if self.controller.groupname is not None:
try:
dgroup = getattr(self.larch.symtable,
self.controller.groupname)
except:
pass
return dgroup
def get_xranges(self, x):
xmin, xmax = min(x), max(x)
i1, i2 = 0, len(x)
_xmin = self.xmin.GetValue()
_xmax = self.xmax.GetValue()
if _xmin > min(x):
i1 = index_of(x, _xmin)
xmin = x[i1]
if _xmax < max(x):
i2 = index_of(x, _xmax) + 1
xmax = x[i2]
xv1 = max(min(x), xmin - (xmax - xmin) / 5.0)
xv2 = min(max(x), xmax + (xmax - xmin) / 5.0)
return i1, i2, xv1, xv2
def build_fitmodel(self):
""" use fit components to build model"""
dgroup = self.get_datagroup()
fullmodel = None
params = Parameters()
self.summary = {'components': [], 'options': {}}
for comp in self.fit_components.values():
if comp.usebox is not None and comp.usebox.IsChecked():
for parwids in comp.parwids.values():
params.add(parwids.param)
self.summary['components'].append(
(comp.mclass.__name__, comp.mclass_kws))
thismodel = comp.mclass(**comp.mclass_kws)
if fullmodel is None:
fullmodel = thismodel
else:
fullmodel += thismodel
self.fit_model = fullmodel
self.fit_params = params
if dgroup is not None:
i1, i2, xv1, xv2 = self.get_xranges(dgroup.x)
xsel = dgroup.x[slice(i1, i2)]
dgroup.xfit = xsel
dgroup.yfit = self.fit_model.eval(self.fit_params, x=xsel)
dgroup.ycomps = self.fit_model.eval_components(
params=self.fit_params, x=xsel)
return dgroup
def onShowModel(self, event=None):
dgroup = self.build_fitmodel()
if dgroup is not None:
with_components = (self.plot_comps.IsChecked()
and len(dgroup.ycomps) > 1)
self.plot_fitmodel(dgroup,
show_resid=False,
with_components=with_components)
def plot_fitmodel(self, dgroup, show_resid=False, with_components=None):
if dgroup is None:
return
i1, i2, xv1, xv2 = self.get_xranges(dgroup.x)
ysel = dgroup.y[slice(i1, i2)]
plotframe = self.controller.get_display(stacked=True)
plotframe.plot(dgroup.xfit,
ysel,
new=True,
panel='top',
xmin=xv1,
xmax=xv2,
label='data',
xlabel=dgroup.plot_xlabel,
ylabel=dgroup.plot_ylabel,
title='Larch XYFit: %s' % dgroup.filename)
plotframe.oplot(dgroup.xfit, dgroup.yfit, label='fit')
plotframe.plot(dgroup.xfit,
ysel - dgroup.yfit,
grid=False,
marker='o',
markersize=4,
linewidth=1,
panel='bot')
if with_components is None:
with_components = (self.plot_comps.IsChecked()
and len(dgroup.ycomps) > 1)
if with_components:
for label, _y in dgroup.ycomps.items():
plotframe.oplot(dgroup.xfit,
_y,
label=label,
style='short dashed')
line_opts = dict(color='#AAAAAA',
label='_nolegend_',
linewidth=1,
zorder=-5)
plotframe.panel_bot.axes.axhline(0, **line_opts)
axvline = plotframe.panel.axes.axvline
if i1 > 0:
axvline(dgroup.x[i1], **line_opts)
if i2 < len(dgroup.x):
axvline(dgroup.x[i2 - 1], **line_opts)
plotframe.panel.canvas.draw()
def onRunFit(self, event=None):
dgroup = self.build_fitmodel()
if dgroup is None:
return
i1, i2, xv1, xv2 = self.get_xranges(dgroup.x)
dgroup.xfit = dgroup.x[slice(i1, i2)]
ysel = dgroup.y[slice(i1, i2)]
weights = np.ones(len(ysel))
if hasattr(dgroup, 'yerr'):
yerr = dgroup.yerr
if not isinstance(yerr, np.ndarray):
yerr = yerr * np.ones(len(ysel))
else:
yerr = yerr[slice(i1, i2)]
yerr_min = 1.e-9 * ysel.mean()
yerr[np.where(yerr < yerr_min)] = yerr_min
weights = 1.0 / yerr
result = self.fit_model.fit(ysel,
params=self.fit_params,
x=dgroup.xfit,
weights=weights,
method='leastsq')
self.summary['xmin'] = xv1
self.summary['xmax'] = xv2
for attr in ('aic', 'bic', 'chisqr', 'redchi', 'ci_out', 'covar',
'flatchain', 'success', 'nan_policy', 'nfev', 'ndata',
'nfree', 'nvarys', 'init_values'):
self.summary[attr] = getattr(result, attr)
self.summary['params'] = result.params
dgroup.fit_history = []
dgroup.fit_history.append(self.summary)
dgroup.yfit = result.best_fit
dgroup.ycomps = self.fit_model.eval_components(params=result.params,
x=dgroup.xfit)
with_components = (self.plot_comps.IsChecked()
and len(dgroup.ycomps) > 1)
self.plot_fitmodel(dgroup,
show_resid=True,
with_components=with_components)
# print(" == fit model == ", self.fit_model)
# print(" == fit result == ", result)
model_repr = self.fit_model._reprstring(long=True)
report = fit_report(result,
show_correl=True,
min_correl=0.25,
sort_pars=True)
report = '[[Model]]\n %s\n%s\n' % (model_repr, report)
self.summary['report'] = report
self.controller.show_report(report)
# fill parameters with best fit values
allparwids = {}
for comp in self.fit_components.values():
if comp.usebox is not None and comp.usebox.IsChecked():
for name, parwids in comp.parwids.items():
allparwids[name] = parwids
for pname, par in result.params.items():
if pname in allparwids:
allparwids[pname].value.SetValue(par.value)
class DemoFrame(wx.Frame):
def __init__(self):
wx.Frame.__init__(self,
None,
-1,
'wxutil demo',
style=wx.DEFAULT_FRAME_STYLE | wx.RESIZE_BORDER
| wx.TAB_TRAVERSAL)
self.SetTitle('wxutil demo')
self.SetFont(Font(11))
self.set_menu()
self.statusbar = self.CreateStatusBar(2, 1)
self.statusbar.SetStatusWidths([-2, -1])
statusbar_fields = ['Initializing....', ' ']
for i in range(len(statusbar_fields)):
self.statusbar.SetStatusText(statusbar_fields[i], i)
self.Bind(wx.EVT_CLOSE, self.onExit)
panel = GridPanel(self, nrows=8, ncols=4)
tctrl_name = TextCtrl(panel,
value='',
action=self.onName,
size=(250, -1))
lctrl_addr = LabeledTextCtrl(self,
value='<>',
action=self.onAddr,
labeltext=' Address: ',
size=(250, -1))
lab3 = HyperText(panel,
' FloatCtrl: ',
size=(100, -1),
action=self.onHyperText)
val3 = FloatCtrl(panel,
'3',
action=self.onFloat1,
precision=2,
minval=0,
maxval=1000,
size=(250, -1))
lab4 = HyperText(panel,
' FloatSpin: ',
size=(100, -1),
action=self.onHyperText)
val4 = FloatSpin(panel,
'12.2',
action=self.onFloatSpin,
digits=2,
increment=0.1,
size=(250, -1))
labx = HyperText(panel,
' NumericCombo: ',
size=(100, -1),
action=self.onHyperText)
steps = make_steps(prec=1, tmin=0, tmax=100)
valx = NumericCombo(panel, steps, precision=1)
self.choice1 = Choice(panel, size=(200, -1), action=self.onChoice)
self.choice1.SetChoices(['Apple', 'Banana', 'Cherry'])
yesno = YesNo(panel)
check1 = Check(panel, label='enable? ', action=self.onCheck)
btn1 = Button(panel,
label='Start',
size=(100, -1),
action=self.onStart)
pinbtn = BitmapButton(panel,
get_icon('pin'),
size=(50, -1),
action=partial(self.onBMButton, opt='pin1'),
tooltip='use last point selected from plot')
togbtn = ToggleButton(panel,
'Press Me',
action=self.onToggleButton,
size=(100, -1),
tooltip='do it, do it now, you will like it')
browse_btn = Button(panel,
'Open File',
action=self.onFileOpen,
size=(150, -1))
okcancel = OkCancel(panel, onOK=self.onOK, onCancel=self.onCancel)
ptable_btn = Button(panel,
'Show Periodic Table',
action=self.onPTable,
size=(175, -1))
edlist_btn = Button(panel,
'Show Editable Listbox',
action=self.onEdList,
size=(175, -1))
filelist_btn = Button(panel,
'Show File CheckList',
action=self.onFileList,
size=(175, -1))
panel.AddText(' Name: ', style=LEFT)
panel.Add(tctrl_name, dcol=2)
panel.Add(lctrl_addr.label, newrow=True)
panel.Add(lctrl_addr, dcol=2)
panel.Add(lab3, newrow=True)
panel.Add(val3, dcol=3)
panel.Add(lab4, newrow=True)
panel.Add(val4, dcol=3)
panel.Add(labx, newrow=True)
panel.Add(valx, dcol=3)
panel.AddText(' Choice : ', newrow=True)
panel.Add(check1)
panel.Add(self.choice1)
panel.AddText(' Yes or No: ', newrow=True)
panel.Add(yesno)
panel.Add(HLine(panel, size=(500, -1)), dcol=3, newrow=True)
panel.Add(btn1, newrow=True)
panel.Add(pinbtn)
panel.Add(togbtn)
panel.Add(browse_btn, newrow=True)
panel.Add(ptable_btn)
panel.Add(edlist_btn, newrow=True)
panel.Add(filelist_btn)
panel.Add(okcancel, newrow=True)
panel.pack()
self.timer = wx.Timer(self)
self.last_time = time.time()
self.Bind(wx.EVT_TIMER, self.onTimer, self.timer)
fsizer = wx.BoxSizer(wx.VERTICAL)
fsizer.Add(panel, 0, LEFT | wx.EXPAND)
wx.CallAfter(self.init_timer)
psize = panel.GetBestSize()
self.SetSize((psize[0] + 5, psize[1] + 25))
pack(self, fsizer)
self.Refresh()
def init_timer(self):
self.timer.Start(500)
def onTimer(self, event):
idle_time = (time.time() - self.last_time)
msg = "Time remaining = %.1f sec" % (30 - idle_time)
self.statusbar.SetStatusText(msg, 1)
if (time.time() - self.last_time) > 30:
print("quitting...")
self.onExit()
def report(self, reason, value):
self.statusbar.SetStatusText("%s: %s" % (reason, value), 0)
self.last_time = time.time()
def set_menu(self):
menu = wx.Menu()
mexit = MenuItem(self, menu, "Q&uit", "Quit Program", self.onExit)
menubar = wx.MenuBar()
menubar.Append(menu, "&File")
self.SetMenuBar(menubar)
def onOK(self, event=None):
self.report("on OK: ", '')
def onCancel(self, event=None):
self.report("on Cancel: ", '')
def onName(self, event=None):
self.report("on Name: ", event)
def onAddr(self, event=None):
self.report("on Addr: ", event)
def onHyperText(self, event=None, label=None):
self.report("on HyperText ", label)
def onFloat1(self, value=None):
self.report("on Float1 ", value)
def onFloatSpin(self, event=None):
self.report("on FloatSpin ", event.GetString())
def onChoice(self, event=None):
self.report("on Choice ", event.GetString())
def onCheck(self, event=None):
self.report("on Check ", event.IsChecked())
self.choice1.Enable(event.IsChecked())
def onStart(self, event=None):
self.report("on Start Button ", '')
def onBMButton(self, event=None, opt='xxx'):
self.report("on Bitmap Button ", opt)
def onToggleButton(self, event=None):
self.report(" on Toggle Button %s " % event.GetString(),
event.IsChecked())
def onPTable(self, event=None):
PTableFrame(fontsize=10).Show()
def onEdList(self, event=None):
frame = wx.Frame(self)
edlist = EditableListBox(frame, self.onEdListSelect)
edlist.Append(" Item 1 ")
edlist.Append(" Item 2 ")
edlist.Append(" Next ")
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add(edlist, 1, wx.EXPAND | wx.ALL, 5)
pack(frame, sizer)
frame.Show()
frame.Raise()
def onEdListSelect(self, event=None, **kws):
self.report(" Editable List selected ", event.GetString())
def onFileList(self, event=None):
frame = wx.Frame(self)
edlist = FileCheckList(frame, select_action=self.onFileListSelect)
for i in range(8):
edlist.Append("File.%3.3d" % (i + 1))
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add(edlist, 1, wx.EXPAND | wx.ALL, 5)
pack(frame, sizer)
frame.Show()
frame.Raise()
def onFileListSelect(self, event=None, **kws):
self.report(" File List selected ", event.GetString())
def onFileOpen(self, event=None):
wildcards = "%s|%s" % (PY_FILES, ALL_FILES)
dlg = wx.FileDialog(self,
message='Select File',
wildcard=wildcards,
style=wx.FD_OPEN)
if dlg.ShowModal() == wx.ID_OK:
path = os.path.abspath(dlg.GetPath())
self.report("file ", path)
dlg.Destroy()
def onExit(self, event=None):
self.Destroy()