def createMainPanel(self):
display0 = wx.Display(0)
client_area = display0.ClientArea
xmin, ymin, xmax, ymax = client_area
xpos = int((xmax-xmin)*0.02) + xmin
ypos = int((ymax-ymin)*0.04) + ymin
self.SetPosition((xpos, ypos))
splitter = wx.SplitterWindow(self, style=wx.SP_LIVE_UPDATE)
splitter.SetMinimumPaneSize(250)
leftpanel = wx.Panel(splitter)
ltop = wx.Panel(leftpanel)
def Btn(msg, x, act):
b = Button(ltop, msg, size=(x, 30), action=act)
b.SetFont(Font(FONTSIZE))
return b
sel_none = Btn('Select None', 120, self.onSelNone)
sel_all = Btn('Select All', 120, self.onSelAll)
self.controller.filelist = FileCheckList(leftpanel,
# main=self,
select_action=self.ShowFile,
remove_action=self.RemoveFile)
tsizer = wx.BoxSizer(wx.HORIZONTAL)
tsizer.Add(sel_all, 1, LCEN|wx.GROW, 1)
tsizer.Add(sel_none, 1, LCEN|wx.GROW, 1)
pack(ltop, tsizer)
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add(ltop, 0, LCEN|wx.GROW, 1)
sizer.Add(self.controller.filelist, 1, LCEN|wx.GROW|wx.ALL, 1)
pack(leftpanel, sizer)
# right hand side
panel = wx.Panel(splitter)
sizer = wx.BoxSizer(wx.VERTICAL)
self.title = SimpleText(panel, 'initializing...', size=(300, -1))
self.title.SetFont(Font(FONTSIZE+2))
ir = 0
sizer.Add(self.title, 0, LCEN|wx.GROW|wx.ALL, 1)
self.nb = flatnotebook(panel, NB_PANELS,
panelkws=dict(controller=self.controller),
on_change=self.onNBChanged)
sizer.Add(self.nb, 1, LCEN|wx.EXPAND, 2)
pack(panel, sizer)
splitter.SplitVertically(leftpanel, panel, 1)
wx.CallAfter(self.init_larch)
def build_display(self):
"""build display"""
self.panel.Add(SimpleText(self.panel, self.title, **titleopts),
dcol=7)
self.panel.Add(SimpleText(self.panel, ' coming soon....'),
dcol=7, newrow=True)
self.panel.pack()
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add(self.panel, 1, wx.LEFT|wx.CENTER, 3)
pack(self, sizer)
def add_text(text, dcol=1, newrow=True):
pan.Add(SimpleText(pan, text), dcol=dcol, newrow=newrow)
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)
pan = self.panel = GridPanel(self, ncols=4, nrows=4, pad=2, itemstyle=LCEN)
self.wids = {}
def FloatSpinWithPin(name, value, **kws):
s = wx.BoxSizer(wx.HORIZONTAL)
self.wids[name] = FloatSpin(pan, value=value, **kws)
bb = BitmapButton(pan, get_icon('pin'), size=(25, 25),
action=partial(self.onSelPoint, opt=name),
tooltip='use last point selected from plot')
s.Add(self.wids[name])
s.Add(bb)
return s
opts = dict(digits=2, increment=0.1)
ppeak_e0 = FloatSpinWithPin('ppeak_e0', value=0, **opts)
ppeak_elo = FloatSpinWithPin('ppeak_elo', value=-15, **opts)
ppeak_ehi = FloatSpinWithPin('ppeak_ehi', value=-5, **opts)
ppeak_emin = FloatSpinWithPin('ppeak_emin', value=-30, **opts)
ppeak_emax = FloatSpinWithPin('ppeak_emax', value=0, **opts)
self.fitbline_btn = Button(pan,'Fit Baseline', action=self.onFitBaseline,
size=(150, 25))
self.fitmodel_btn = Button(pan, 'Fit Model',
action=self.onFitModel, size=(150, 25))
self.fitsel_btn = Button(pan, 'Fit Selected Groups',
action=self.onFitSelected, size=(150, 25))
self.fitmodel_btn.Disable()
self.fitsel_btn.Disable()
self.array_choice = Choice(pan, size=(150, -1),
choices=list(Array_Choices.keys()))
self.array_choice.SetSelection(1)
models_peaks = Choice(pan, size=(150, -1),
choices=ModelChoices['peaks'],
action=self.addModel)
models_other = Choice(pan, size=(150, -1),
choices=ModelChoices['other'],
action=self.addModel)
self.plot_choice = Choice(pan, size=(150, -1),
choices=PlotChoices,
action=self.onPlot)
self.message = SimpleText(pan,
'first fit baseline, then add peaks to fit model.')
self.msg_centroid = SimpleText(pan, '----')
opts = dict(default=True, size=(75, -1), action=self.onPlot)
self.show_centroid = Check(pan, label='show?', **opts)
self.show_peakrange = Check(pan, label='show?', **opts)
self.show_fitrange = Check(pan, label='show?', **opts)
self.show_e0 = Check(pan, label='show?', **opts)
opts = dict(default=False, size=(200, -1), action=self.onPlot)
self.plot_sub_bline = Check(pan, label='Subtract Baseline?', **opts)
def add_text(text, dcol=1, newrow=True):
pan.Add(SimpleText(pan, text), dcol=dcol, newrow=newrow)
titleopts = dict(font=Font(12), colour='#AA0000')
pan.Add(SimpleText(pan, ' Pre-edge Peak Fitting', **titleopts), dcol=5)
add_text(' Run Fit:', newrow=False)
add_text('Array to fit: ')
pan.Add(self.array_choice, dcol=3)
pan.Add((10, 10))
pan.Add(self.fitbline_btn)
add_text('E0: ')
pan.Add(ppeak_e0)
pan.Add((10, 10), dcol=2)
pan.Add(self.show_e0)
pan.Add(self.fitmodel_btn)
add_text('Fit Energy Range: ')
pan.Add(ppeak_emin)
add_text(' : ', newrow=False)
pan.Add(ppeak_emax)
pan.Add(self.show_fitrange)
pan.Add(self.fitsel_btn)
t = SimpleText(pan, 'Pre-edge Peak Range: ')
t.SetToolTip('Range used as mask for background')
pan.Add(t, newrow=True)
pan.Add(ppeak_elo)
add_text(' : ', newrow=False)
pan.Add(ppeak_ehi)
pan.Add(self.show_peakrange)
add_text( 'Peak Centroid: ')
pan.Add(self.msg_centroid, dcol=3)
pan.Add(self.show_centroid, dcol=1)
# plot buttons
ts = wx.BoxSizer(wx.HORIZONTAL)
ts.Add(self.plot_choice)
ts.Add(self.plot_sub_bline)
pan.Add(SimpleText(pan, 'Plot: '), newrow=True)
pan.Add(ts, dcol=7)
# add model
ts = wx.BoxSizer(wx.HORIZONTAL)
ts.Add(models_peaks)
ts.Add(models_other)
pan.Add(SimpleText(pan, 'Add Component: '), newrow=True)
pan.Add(ts, dcol=7)
pan.Add(SimpleText(pan, 'Messages: '), newrow=True)
pan.Add(self.message, dcol=7)
pan.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(pan, 0, LCEN, 3)
sizer.Add((5,5), 0, LCEN, 3)
sizer.Add(HLine(self, size=(550, 2)), 0, LCEN, 3)
sizer.Add((5,5), 0, LCEN, 3)
sizer.Add(self.mod_nb, 1, LCEN|wx.GROW, 10)
pack(self, sizer)
class PrePeakPanel(wx.Panel):
def __init__(self, parent=None, controller=None, **kws):
wx.Panel.__init__(self, parent, -1, size=(550, 625), **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 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)
# print(" Fill prepeak panel from group ", fname, gname, dgroup)
self.fill_form(dgroup)
except:
pass # print(" Cannot Fill prepeak panel from group ")
def larch_eval(self, cmd):
"""eval"""
self.controller.larch.eval(cmd)
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)
pan = self.panel = GridPanel(self, ncols=4, nrows=4, pad=2, itemstyle=LCEN)
self.wids = {}
def FloatSpinWithPin(name, value, **kws):
s = wx.BoxSizer(wx.HORIZONTAL)
self.wids[name] = FloatSpin(pan, value=value, **kws)
bb = BitmapButton(pan, get_icon('pin'), size=(25, 25),
action=partial(self.onSelPoint, opt=name),
tooltip='use last point selected from plot')
s.Add(self.wids[name])
s.Add(bb)
return s
opts = dict(digits=2, increment=0.1)
ppeak_e0 = FloatSpinWithPin('ppeak_e0', value=0, **opts)
ppeak_elo = FloatSpinWithPin('ppeak_elo', value=-15, **opts)
ppeak_ehi = FloatSpinWithPin('ppeak_ehi', value=-5, **opts)
ppeak_emin = FloatSpinWithPin('ppeak_emin', value=-30, **opts)
ppeak_emax = FloatSpinWithPin('ppeak_emax', value=0, **opts)
self.fitbline_btn = Button(pan,'Fit Baseline', action=self.onFitBaseline,
size=(150, 25))
self.fitmodel_btn = Button(pan, 'Fit Model',
action=self.onFitModel, size=(150, 25))
self.fitsel_btn = Button(pan, 'Fit Selected Groups',
action=self.onFitSelected, size=(150, 25))
self.fitmodel_btn.Disable()
self.fitsel_btn.Disable()
self.array_choice = Choice(pan, size=(150, -1),
choices=list(Array_Choices.keys()))
self.array_choice.SetSelection(1)
models_peaks = Choice(pan, size=(150, -1),
choices=ModelChoices['peaks'],
action=self.addModel)
models_other = Choice(pan, size=(150, -1),
choices=ModelChoices['other'],
action=self.addModel)
self.plot_choice = Choice(pan, size=(150, -1),
choices=PlotChoices,
action=self.onPlot)
self.message = SimpleText(pan,
'first fit baseline, then add peaks to fit model.')
self.msg_centroid = SimpleText(pan, '----')
opts = dict(default=True, size=(75, -1), action=self.onPlot)
self.show_centroid = Check(pan, label='show?', **opts)
self.show_peakrange = Check(pan, label='show?', **opts)
self.show_fitrange = Check(pan, label='show?', **opts)
self.show_e0 = Check(pan, label='show?', **opts)
opts = dict(default=False, size=(200, -1), action=self.onPlot)
self.plot_sub_bline = Check(pan, label='Subtract Baseline?', **opts)
def add_text(text, dcol=1, newrow=True):
pan.Add(SimpleText(pan, text), dcol=dcol, newrow=newrow)
titleopts = dict(font=Font(12), colour='#AA0000')
pan.Add(SimpleText(pan, ' Pre-edge Peak Fitting', **titleopts), dcol=5)
add_text(' Run Fit:', newrow=False)
add_text('Array to fit: ')
pan.Add(self.array_choice, dcol=3)
pan.Add((10, 10))
pan.Add(self.fitbline_btn)
add_text('E0: ')
pan.Add(ppeak_e0)
pan.Add((10, 10), dcol=2)
pan.Add(self.show_e0)
pan.Add(self.fitmodel_btn)
add_text('Fit Energy Range: ')
pan.Add(ppeak_emin)
add_text(' : ', newrow=False)
pan.Add(ppeak_emax)
pan.Add(self.show_fitrange)
pan.Add(self.fitsel_btn)
t = SimpleText(pan, 'Pre-edge Peak Range: ')
t.SetToolTip('Range used as mask for background')
pan.Add(t, newrow=True)
pan.Add(ppeak_elo)
add_text(' : ', newrow=False)
pan.Add(ppeak_ehi)
pan.Add(self.show_peakrange)
add_text( 'Peak Centroid: ')
pan.Add(self.msg_centroid, dcol=3)
pan.Add(self.show_centroid, dcol=1)
# plot buttons
ts = wx.BoxSizer(wx.HORIZONTAL)
ts.Add(self.plot_choice)
ts.Add(self.plot_sub_bline)
pan.Add(SimpleText(pan, 'Plot: '), newrow=True)
pan.Add(ts, dcol=7)
# add model
ts = wx.BoxSizer(wx.HORIZONTAL)
ts.Add(models_peaks)
ts.Add(models_other)
pan.Add(SimpleText(pan, 'Add Component: '), newrow=True)
pan.Add(ts, dcol=7)
pan.Add(SimpleText(pan, 'Messages: '), newrow=True)
pan.Add(self.message, dcol=7)
pan.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(pan, 0, LCEN, 3)
sizer.Add((5,5), 0, LCEN, 3)
sizer.Add(HLine(self, size=(550, 2)), 0, LCEN, 3)
sizer.Add((5,5), 0, LCEN, 3)
sizer.Add(self.mod_nb, 1, LCEN|wx.GROW, 10)
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, 'prepeak_config', {})
if 'e0' not in conf:
conf = dict(e0 = dgroup.e0, elo=-10, ehi=-5,
emin=-40, emax=0, yarray='norm')
dgroup.prepeak_config = conf
if not hasattr(dgroup, 'prepeaks'):
dgroup.prepeaks = Group()
return conf
def fill_form(self, dat):
if isinstance(dat, Group):
self.wids['ppeak_e0'].SetValue(dat.e0)
if hasattr(dat, 'prepeaks'):
self.wids['ppeak_emin'].SetValue(dat.prepeaks.emin)
self.wids['ppeak_emax'].SetValue(dat.prepeaks.emax)
self.wids['ppeak_elo'].SetValue(dat.prepeaks.elo)
self.wids['ppeak_ehi'].SetValue(dat.prepeaks.ehi)
elif instance(dat, dict):
self.wids['ppeak_e0'].SetValue(dat['e0'])
self.wids['ppeak_emin'].SetValue(dat['emin'])
self.wids['ppeak_emax'].SetValue(dat['emax'])
self.wids['ppeak_elo'].SetValue(dat['elo'])
self.wids['ppeak_ehi'].SetValue(dat['ehi'])
self.array_choice.SetStringSelection(dat['array_desc'])
self.show_e0.Enable(dat['show_e0'])
self.show_centroid.Enable(dat['show_centroid'])
self.show_fitrange.Enable(dat['show_fitrange'])
self.show_peakrange.Enable(dat['show_peakrange'])
self.plot_sub_bline.Enable(dat['plot_sub_bline'])
def read_form(self):
"read for, returning dict of values"
dgroup = self.controller.get_group()
array_desc = self.array_choice.GetStringSelection()
form_opts = {'gname': dgroup.groupname,
'array_desc': array_desc.lower(),
'array_name': Array_Choices[array_desc],
'baseline_form': 'lorentzian'}
form_opts['e0'] = self.wids['ppeak_e0'].GetValue()
form_opts['emin'] = self.wids['ppeak_emin'].GetValue()
form_opts['emax'] = self.wids['ppeak_emax'].GetValue()
form_opts['elo'] = self.wids['ppeak_elo'].GetValue()
form_opts['ehi'] = self.wids['ppeak_ehi'].GetValue()
form_opts['plot_sub_bline'] = self.plot_sub_bline.IsChecked()
form_opts['show_centroid'] = self.show_centroid.IsChecked()
form_opts['show_peakrange'] = self.show_peakrange.IsChecked()
form_opts['show_fitrange'] = self.show_fitrange.IsChecked()
form_opts['show_e0'] = self.show_e0.IsChecked()
return form_opts
def onFitBaseline(self, evt=None):
opts = self.read_form()
cmd = """{gname:s}.ydat = 1.0*{gname:s}.{array_name:s}
pre_edge_baseline(energy={gname:s}.energy, norm={gname:s}.ydat, group={gname:s},
form='{baseline_form:s}', with_line=True,
elo={elo:.3f}, ehi={ehi:.3f}, emin={emin:.3f}, emax={emax:.3f})
"""
self.larch_eval(cmd.format(**opts))
dgroup = self.controller.get_group()
ppeaks = dgroup.prepeaks
dgroup.centroid_msg = "%.4f +/- %.4f eV" % (ppeaks.centroid,
ppeaks.delta_centroid)
self.msg_centroid.SetLabel(dgroup.centroid_msg)
if 'loren_' not in self.fit_components:
self.addModel(model='Lorentzian', prefix='loren_', isbkg=True)
if 'line_' not in self.fit_components:
self.addModel(model='Linear', prefix='line_', isbkg=True)
for prefix in ('loren_', 'line_'):
cmp = self.fit_components[prefix]
# cmp.bkgbox.SetValue(1)
self.fill_model_params(prefix, dgroup.prepeaks.fit_details.params)
self.fill_form(dgroup)
self.fitmodel_btn.Enable()
# self.fitallmodel_btn.Enable()
i1, i2 = self.get_xranges(dgroup.energy)
dgroup.yfit = dgroup.xfit = 0.0*dgroup.energy[i1:i2]
self.plot_choice.SetStringSelection(PLOT_BASELINE)
self.onPlot()
def fill_model_params(self, prefix, params):
comp = self.fit_components[prefix]
parwids = comp.parwids
for pname, par in params.items():
pname = prefix + pname
if pname in parwids:
wids = parwids[pname]
if wids.minval is not None:
wids.minval.SetValue(par.min)
if wids.maxval is not None:
wids.maxval.SetValue(par.max)
wids.value.SetValue(par.value)
varstr = 'vary' if par.vary else 'fix'
if par.expr is not None:
varstr = 'constrain'
if wids.vary is not None:
wids.vary.SetStringSelection(varstr)
def onPlot(self, evt=None):
plot_choice = self.plot_choice.GetStringSelection()
opts = self.read_form()
dgroup = self.controller.get_group()
ppeaks = getattr(dgroup, 'prepeaks', None)
if ppeaks is None:
return
i1, i2 = self.get_xranges(dgroup.xdat)
# i2 = len(ppeaks.baseline) + i1
if len(dgroup.yfit) > len(ppeaks.baseline):
i2 = i1 + len(ppeaks.baseline)
# print(" Indexes: ", i1, i2, i2-i1, len(dgroup.yfit), len(ppeaks.baseline))
xdat = 1.0*dgroup.energy
ydat = 1.0*dgroup.ydat
yfit = 1.0*dgroup.ydat
baseline = 1.0*dgroup.ydat
yfit[i1:i2] = dgroup.yfit[:i2-i1]
baseline[i1:i2] = ppeaks.baseline[:i2-i1]
if opts['plot_sub_bline']:
ydat = ydat - baseline
if plot_choice in (PLOT_FIT, PLOT_RESID):
yfit = yfit - baseline
if plot_choice == PLOT_RESID:
resid = ydat - yfit
_xs = dgroup.energy[i1:i2]
xrange = max(_xs) - min(_xs)
pxmin = min(_xs) - 0.05 * xrange
pxmax = max(_xs) + 0.05 * xrange
jmin = index_of(dgroup.energy, pxmin)
jmax = index_of(dgroup.energy, pxmax) + 1
_ys = ydat[jmin:jmax]
yrange = max(_ys) - min(_ys)
pymin = min(_ys) - 0.05 * yrange
pymax = max(_ys) + 0.05 * yrange
title = ' pre-edge fit'
if plot_choice == PLOT_BASELINE:
title = ' pre-edge baseline'
if opts['plot_sub_bline']:
title = ' pre-edge peaks'
array_desc = self.array_choice.GetStringSelection()
plotopts = {'xmin': pxmin, 'xmax': pxmax,
'ymin': pymin, 'ymax': pymax,
'title': '%s: %s' % (opts['gname'], title),
'xlabel': 'Energy (eV)',
'ylabel': '%s $\mu$' % opts['array_desc'],
'label': '%s $\mu$' % opts['array_desc'],
'delay_draw': True,
'show_legend': True}
plot_extras = []
if opts['show_fitrange']:
popts = {'color': '#DDDDCC'}
emin = opts['emin']
emax = opts['emax']
imin = index_of(dgroup.energy, emin)
imax = index_of(dgroup.energy, emax)
plot_extras.append(('vline', emin, None, popts))
plot_extras.append(('vline', emax, None, popts))
if opts['show_peakrange']:
popts = {'marker': '+', 'markersize': 6}
elo = opts['elo']
ehi = opts['ehi']
ilo = index_of(dgroup.xdat, elo)
ihi = index_of(dgroup.xdat, ehi)
plot_extras.append(('marker', elo, ydat[ilo], popts))
plot_extras.append(('marker', ehi, ydat[ihi], popts))
if opts['show_centroid']:
popts = {'color': '#EECCCC'}
ecen = getattr(dgroup.prepeaks, 'centroid', -1)
if ecen > min(dgroup.energy):
plot_extras.append(('vline', ecen, None, popts))
pframe = self.controller.get_display(win=2,
stacked=(plot_choice==PLOT_RESID))
ppanel = pframe.panel
axes = ppanel.axes
plotopts.update(PLOTOPTS_1)
ppanel.plot(xdat, ydat, **plotopts)
if plot_choice == PLOT_BASELINE:
if not opts['plot_sub_bline']:
ppanel.oplot(dgroup.prepeaks.energy,
dgroup.prepeaks.baseline,
label='baseline', **PLOTOPTS_2)
elif plot_choice in (PLOT_FIT, PLOT_RESID):
ppanel.oplot(dgroup.energy, yfit,
label='fit', **PLOTOPTS_1)
if hasattr(dgroup, 'ycomps'):
ncomp = len(dgroup.ycomps)
icomp = 0
for label, ycomp in dgroup.ycomps.items():
icomp +=1
fcomp = self.fit_components[label]
# print("ycomp: ", plot_choice, label, len(ycomp), len(dgroup.xfit),
# fcomp.bkgbox.IsChecked(), opts['plot_sub_bline'], icomp, ncomp)
if not (fcomp.bkgbox.IsChecked() and opts['plot_sub_bline']):
ppanel.oplot(dgroup.xfit, ycomp, label=label,
delay_draw=(icomp!=ncomp), style='short dashed')
if plot_choice == PLOT_RESID:
_ys = resid
yrange = max(_ys) - min(_ys)
plotopts['ymin'] = min(_ys) - 0.05 * yrange
plotopts['ymax'] = max(_ys) + 0.05 * yrange
plotopts['delay_draw'] = False
plotopts['ylabel'] = 'data-fit'
plotopts['label'] = '_nolegend_'
pframe.plot(dgroup.energy, resid, panel='bot', **plotopts)
pframe.Show()
# print(" RESIDUAL PLOT margins: ")
# print(" top : ", pframe.panel.conf.margins)
# print(" bot : ", pframe.panel_bot.conf.margins)
for etype, x, y, opts in plot_extras:
if etype == 'marker':
popts = {'marker': 'o', 'markersize': 4,
'label': '_nolegend_',
'markerfacecolor': 'red',
'markeredgecolor': '#884444'}
popts.update(opts)
axes.plot([x], [y], **popts)
elif etype == 'vline':
popts = {'ymin': 0, 'ymax': 1.0, 'color': '#888888',
'label': '_nolegend_'}
popts.update(opts)
axes.axvline(x, **popts)
ppanel.canvas.draw()
def onNBChanged(self, event=None):
idx = self.mod_nb.GetSelection()
def addModel(self, event=None, model=None, prefix=None, isbkg=False):
if model is None and event is not None:
model = event.GetString()
if model is None or model.startswith('<'):
return
if prefix is None:
p = model[:5].lower()
curmodels = ["%s%i_" % (p, 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)
title = prefix[:-1]
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:
if model in ModelFuncs:
mclass = getattr(lm_models, ModelFuncs[model])
else:
mclass = getattr(lm_models, model+'Model')
minst = mclass(prefix=prefix)
panel = GridPanel(self.mod_nb, ncols=2, nrows=5, pad=2, 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 in Fit?', size=(100, -1))
bkgbox = Check(panel, default=False, label='Is Baseline?', size=(125, -1))
if isbkg:
bkgbox.SetValue(1)
delbtn = Button(panel, 'Delete Component', size=(125, -1),
action=partial(self.onDeleteComponent, prefix=prefix))
pick2msg = SimpleText(panel, " ", size=(125, -1))
pick2btn = Button(panel, 'Pick Values from Data', size=(150, -1),
action=partial(self.onPick2Points, prefix=prefix))
# SetTip(mname, 'Label for the model component')
SetTip(usebox, 'Use this component in fit?')
SetTip(bkgbox, 'Label this component as "background" when plotting?')
SetTip(delbtn, 'Delete this model component')
SetTip(pick2btn, 'Select X range on Plot to Guess Initial Values')
panel.Add(SLabel(label, size=(275, -1), colour='#0000AA'),
dcol=3, style=wx.ALIGN_LEFT, newrow=True)
panel.Add(usebox, dcol=1)
panel.Add(bkgbox, dcol=2, style=LCEN)
panel.Add(delbtn, dcol=1, style=wx.ALIGN_LEFT)
panel.Add(pick2btn, dcol=2, style=wx.ALIGN_LEFT, newrow=True)
panel.Add(pick2msg, dcol=2, style=wx.ALIGN_RIGHT)
# panel.Add((10, 10), newrow=True)
# panel.Add(HLine(panel, size=(150, 3)), dcol=4, style=wx.ALIGN_CENTER)
panel.Add(SLabel("Parameter "), style=wx.ALIGN_LEFT, newrow=True)
panel.AddMany((SLabel(" Value"), SLabel(" Type"), SLabel(' Bounds'),
SLabel(" Min", size=(60, -1)),
SLabel(" Max", size=(60, -1)), 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=100, expr_size=125,
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.bounds,
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=100, expr_size=225,
float_size=80, prefix=prefix,
widgets=('name', 'value', 'expr'))
parwids[par.name] = pwids
panel.Add(pwids.name, newrow=True)
panel.Add(pwids.value)
panel.Add(pwids.expr, dcol=4, style=wx.ALIGN_RIGHT)
pwids.value.Disable()
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, bkgbox=bkgbox)
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()
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.xdat, dgroup.ydat
i0 = index_of(dgroup.xdat, xmin)
i1 = index_of(dgroup.xdat, xmax)
x, y = dgroup.xdat[i0:i1+1], dgroup.ydat[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.xdat)
plotframe = self.controller.get_display()
plotframe.cursor_hist = []
plotframe.oplot(dgroup.xdat, 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()
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 onSaveFitResult(self, event=None):
dgroup = self.controller.get_group()
deffile = dgroup.filename.replace('.', '_') + '.modl'
outfile = FileSave(self, 'Save Fit Result',
default_file=deffile,
wildcard=ModelWcards)
if outfile is not None:
try:
self.save_fit_result(dgroup.fit_history[-1], outfile)
except IOError:
print('could not write %s' % outfile)
def onLoadFitResult(self, event=None):
mfile = FileOpen(self, 'Load Fit Result',
default_file='', wildcard=ModelWcards)
if mfile is not None:
self.load_modelresult(mfile)
def save_fit_result(self, fitresult, outfile):
"""saves a customized ModelResult"""
save_modelresult(fitresult, outfile)
def load_modelresult(self, inpfile):
"""read a customized ModelResult"""
result = load_modelresult(inpfile)
for prefix in list(self.fit_components.keys()):
self.onDeleteComponent(self, prefix=prefix)
for comp in result.model.components:
isbkg = comp.prefix in result.user_options['bkg_components']
self.addModel(model=comp.func.__name__,
prefix=comp.prefix, isbkg=isbkg)
for comp in result.model.components:
parwids = self.fit_components[comp.prefix].parwids
for pname, par in result.params.items():
if pname in parwids:
wids = parwids[pname]
if wids.minval is not None:
wids.minval.SetValue(par.min)
if wids.maxval is not None:
wids.maxval.SetValue(par.max)
val = result.init_values.get(pname, par.value)
wids.value.SetValue(val)
self.fill_form(result.user_options)
return result
def onExportFitResult(self, event=None):
dgroup = self.controller.get_group()
deffile = dgroup.filename.replace('.', '_') + '_result.xdi'
wcards = 'All files (*.*)|*.*'
outfile = FileSave(self, 'Export Fit Result',
default_file=deffile, wildcard=wcards)
if outfile is not None:
i1, i2 = self.get_xranges(dgroup.xdat)
x = dgroup.xdat[i1:i2]
y = dgroup.ydat[i1:i2]
yerr = None
if hasattr(dgroup, 'yerr'):
yerr = 1.0*dgroup.yerr
if not isinstance(yerr, np.ndarray):
yerr = yerr * np.ones(len(y))
else:
yerr = yerr[i1:i2]
export_modelresult(dgroup.fit_history[-1],
filename=outfile,
datafile=dgroup.filename,
ydata=y, yerr=yerr, x=x)
def onSelPoint(self, evt=None, opt='__', relative_e0=False, 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 not None:
if relative_e0 and 'e0' in self.wids:
_x -= self.wids['e0'].GetValue()
self.wids[opt].SetValue(_x)
def get_xranges(self, x):
opts = self.read_form()
dgroup = self.controller.get_group()
en_eps = min(np.diff(dgroup.energy)) / 5.
i1 = index_of(x, opts['emin'] + en_eps)
i2 = index_of(x, opts['emax'] + en_eps) + 1
return i1, i2
def build_fitmodel(self):
""" use fit components to build model"""
dgroup = self.controller.get_group()
fullmodel = None
params = Parameters()
self.summary = {'components': [], 'options': {}}
peaks = []
for comp in self.fit_components.values():
_cen, _amp = None, None
if comp.usebox is not None and comp.usebox.IsChecked():
for parwids in comp.parwids.values():
params.add(parwids.param)
#print(" add param ", parwids.param)
if parwids.param.name.endswith('_center'):
_cen = parwids.param.name
elif parwids.param.name.endswith('_amplitude'):
_amp = parwids.param.name
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
if not comp.bkgbox.IsChecked() and _cen is not None and _amp is not None:
peaks.append((_amp, _cen))
if len(peaks) > 0:
denom = '+'.join([p[0] for p in peaks])
numer = '+'.join(["%s*%s "% p for p in peaks])
params.add('fit_centroid', expr="(%s)/(%s)" %(numer, denom))
self.fit_model = fullmodel
self.fit_params = params
if dgroup is not None:
i1, i2 = self.get_xranges(dgroup.xdat)
xsel = dgroup.xdat[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 onFitSelected(self, event=None):
dgroup = self.build_fitmodel()
opts = self.read_form()
print("fitting selected groups in progress")
def onFitModel(self, event=None):
dgroup = self.build_fitmodel()
opts = self.read_form()
i1, i2 = self.get_xranges(dgroup.xdat)
dgroup.xfit = dgroup.xdat[i1:i2]
ysel = dgroup.ydat[i1:i2]
# print('onFit Model : xrange ', i1, i2, len(dgroup.xfit), len(dgroup.yfit))
weights = np.ones(len(ysel))
if hasattr(dgroup, 'yerr'):
yerr = 1.0*dgroup.yerr
if not isinstance(yerr, np.ndarray):
yerr = yerr * np.ones(len(ysel))
else:
yerr = yerr[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'] = dgroup.xdat[i1]
self.summary['xmax'] = dgroup.xdat[i2]
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.yfit = result.best_fit
dgroup.ycomps = self.fit_model.eval_components(params=result.params,
x=dgroup.xfit)
result.model_repr = self.fit_model._reprstring(long=True)
## hacks to save user options
result.user_options = opts
bkg_comps = []
for label, comp in self.fit_components.items():
if comp.bkgbox.IsChecked():
bkg_comps.append(label)
result.user_options['bkg_components'] = bkg_comps
self.autosave_modelresult(result)
if not hasattr(dgroup, 'fit_history'):
dgroup.fit_history = []
dgroup.fit_history.append(result)
self.plot_choice.SetStringSelection(PLOT_FIT)
self.onPlot()
self.parent.show_subframe('prepeak_result_frame', FitResultFrame,
datagroup=dgroup, peakframe=self)
self.parent.subframes['prepeak_result_frame'].show_fitresult()
[m.Enable(True) for m in self.parent.afterfit_menus]
def update_start_values(self, params):
"""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 params.items():
if pname in allparwids:
allparwids[pname].value.SetValue(par.value)
def autosave_modelresult(self, result, fname=None):
"""autosave model result to user larch folder"""
xasguidir = os.path.join(site_config.usr_larchdir, 'xasgui')
if not os.path.exists(xasguidir):
try:
os.makedirs(xasguidir)
except OSError:
print("Warning: cannot create XAS GUI user folder")
return
if not HAS_MODELSAVE:
print("Warning: cannot save model results: upgrade lmfit")
return
if fname is None:
fname = 'autosave.fitresult'
fname = os.path.join(xasguidir, fname)
self.save_fit_result(result, fname)
class PrePeakPanel(TaskPanel):
def __init__(self, parent=None, controller=None, **kws):
TaskPanel.__init__(self, parent, controller,
configname='prepeaks_config',
config=defaults, **kws)
self.fit_components = OrderedDict()
self.user_added_params = None
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 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 # print(" Cannot Fill prepeak panel from group ")
def build_display(self):
self.mod_nb = flatnotebook(self, {})
pan = self.panel = GridPanel(self, ncols=4, nrows=4, pad=2, itemstyle=LEFT)
self.wids = {}
fsopts = dict(digits=2, increment=0.1, with_pin=True)
ppeak_e0 = self.add_floatspin('ppeak_e0', value=0, **fsopts)
ppeak_elo = self.add_floatspin('ppeak_elo', value=-15, **fsopts)
ppeak_ehi = self.add_floatspin('ppeak_ehi', value=-5, **fsopts)
ppeak_emin = self.add_floatspin('ppeak_emin', value=-30, **fsopts)
ppeak_emax = self.add_floatspin('ppeak_emax', value=0, **fsopts)
self.fitbline_btn = Button(pan,'Fit Baseline', action=self.onFitBaseline,
size=(125, -1))
self.plotmodel_btn = Button(pan, 'Plot Model',
action=self.onPlotModel, size=(125, -1))
self.fitmodel_btn = Button(pan, 'Fit Model',
action=self.onFitModel, size=(125, -1))
self.loadmodel_btn = Button(pan, 'Load Model',
action=self.onLoadFitResult, size=(125, -1))
self.fitmodel_btn.Disable()
self.array_choice = Choice(pan, size=(175, -1),
choices=list(Array_Choices.keys()))
self.array_choice.SetSelection(1)
models_peaks = Choice(pan, size=(150, -1),
choices=ModelChoices['peaks'],
action=self.addModel)
models_other = Choice(pan, size=(150, -1),
choices=ModelChoices['other'],
action=self.addModel)
self.models_peaks = models_peaks
self.models_other = models_other
self.message = SimpleText(pan,
'first fit baseline, then add peaks to fit model.')
self.msg_centroid = SimpleText(pan, '----')
opts = dict(default=True, size=(75, -1), action=self.onPlot)
self.show_centroid = Check(pan, label='show?', **opts)
self.show_peakrange = Check(pan, label='show?', **opts)
self.show_fitrange = Check(pan, label='show?', **opts)
self.show_e0 = Check(pan, label='show?', **opts)
opts = dict(default=False, size=(200, -1), action=self.onPlot)
def add_text(text, dcol=1, newrow=True):
pan.Add(SimpleText(pan, text), dcol=dcol, newrow=newrow)
pan.Add(SimpleText(pan, ' Pre-edge Peak Fitting',
**self.titleopts), dcol=5)
add_text(' Run Fit:', newrow=False)
add_text('Array to fit: ')
pan.Add(self.array_choice, dcol=3)
pan.Add((10, 10))
pan.Add(self.fitbline_btn)
add_text('E0: ')
pan.Add(ppeak_e0)
pan.Add((10, 10), dcol=2)
pan.Add(self.show_e0)
pan.Add(self.plotmodel_btn)
add_text('Fit Energy Range: ')
pan.Add(ppeak_emin)
add_text(' : ', newrow=False)
pan.Add(ppeak_emax)
pan.Add(self.show_fitrange)
pan.Add(self.fitmodel_btn)
t = SimpleText(pan, 'Pre-edge Peak Range: ')
SetTip(t, 'Range used as mask for background')
pan.Add(t, newrow=True)
pan.Add(ppeak_elo)
add_text(' : ', newrow=False)
pan.Add(ppeak_ehi)
pan.Add(self.show_peakrange)
# pan.Add(self.fitsel_btn)
add_text( 'Peak Centroid: ')
pan.Add(self.msg_centroid, dcol=3)
pan.Add(self.show_centroid, dcol=1)
pan.Add(self.loadmodel_btn)
# add model
ts = wx.BoxSizer(wx.HORIZONTAL)
ts.Add(models_peaks)
ts.Add(models_other)
pan.Add(SimpleText(pan, 'Add Component: '), newrow=True)
pan.Add(ts, dcol=7)
pan.Add(SimpleText(pan, 'Messages: '), newrow=True)
pan.Add(self.message, dcol=7)
pan.pack()
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add((10, 10), 0, LEFT, 3)
sizer.Add(pan, 0, LEFT, 3)
sizer.Add((10, 10), 0, LEFT, 3)
sizer.Add(HLine(self, size=(550, 2)), 0, LEFT, 3)
sizer.Add((10, 10), 0, LEFT, 3)
sizer.Add(self.mod_nb, 1, LEFT|wx.GROW, 10)
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, 'prepeak_config', {})
if 'e0' not in conf:
conf = defaults
conf['e0'] = getattr(dgroup, 'e0', -1)
dgroup.prepeak_config = conf
if not hasattr(dgroup, 'prepeaks'):
dgroup.prepeaks = Group()
return conf
def fill_form(self, dat):
if isinstance(dat, Group):
self.wids['ppeak_e0'].SetValue(dat.e0)
if hasattr(dat, 'prepeaks'):
self.wids['ppeak_emin'].SetValue(dat.prepeaks.emin)
self.wids['ppeak_emax'].SetValue(dat.prepeaks.emax)
self.wids['ppeak_elo'].SetValue(dat.prepeaks.elo)
self.wids['ppeak_ehi'].SetValue(dat.prepeaks.ehi)
elif isinstance(dat, dict):
self.wids['ppeak_e0'].SetValue(dat['e0'])
self.wids['ppeak_emin'].SetValue(dat['emin'])
self.wids['ppeak_emax'].SetValue(dat['emax'])
self.wids['ppeak_elo'].SetValue(dat['elo'])
self.wids['ppeak_ehi'].SetValue(dat['ehi'])
self.array_choice.SetStringSelection(dat['array_desc'])
self.show_e0.Enable(dat['show_e0'])
self.show_centroid.Enable(dat['show_centroid'])
self.show_fitrange.Enable(dat['show_fitrange'])
self.show_peakrange.Enable(dat['show_peakrange'])
def read_form(self):
"read for, returning dict of values"
dgroup = self.controller.get_group()
array_desc = self.array_choice.GetStringSelection()
form_opts = {'gname': dgroup.groupname,
'filename': dgroup.filename,
'array_desc': array_desc.lower(),
'array_name': Array_Choices[array_desc],
'baseline_form': 'lorentzian',
'bkg_components': []}
form_opts['e0'] = self.wids['ppeak_e0'].GetValue()
form_opts['emin'] = self.wids['ppeak_emin'].GetValue()
form_opts['emax'] = self.wids['ppeak_emax'].GetValue()
form_opts['elo'] = self.wids['ppeak_elo'].GetValue()
form_opts['ehi'] = self.wids['ppeak_ehi'].GetValue()
form_opts['plot_sub_bline'] = False # self.plot_sub_bline.IsChecked()
form_opts['show_centroid'] = self.show_centroid.IsChecked()
form_opts['show_peakrange'] = self.show_peakrange.IsChecked()
form_opts['show_fitrange'] = self.show_fitrange.IsChecked()
form_opts['show_e0'] = self.show_e0.IsChecked()
return form_opts
def onFitBaseline(self, evt=None):
opts = self.read_form()
cmd = """{gname:s}.ydat = 1.0*{gname:s}.{array_name:s}
pre_edge_baseline(energy={gname:s}.energy, norm={gname:s}.ydat, group={gname:s}, form='{baseline_form:s}',
with_line=True, elo={elo:.3f}, ehi={ehi:.3f}, emin={emin:.3f}, emax={emax:.3f})"""
self.larch_eval(cmd.format(**opts))
dgroup = self.controller.get_group()
ppeaks = dgroup.prepeaks
dgroup.centroid_msg = "%.4f +/- %.4f eV" % (ppeaks.centroid,
ppeaks.delta_centroid)
self.msg_centroid.SetLabel(dgroup.centroid_msg)
if 'bpeak_' not in self.fit_components:
self.addModel(model='Lorentzian', prefix='bpeak_', isbkg=True)
if 'bline_' not in self.fit_components:
self.addModel(model='Linear', prefix='bline_', isbkg=True)
for prefix in ('bpeak_', 'bline_'):
cmp = self.fit_components[prefix]
# cmp.bkgbox.SetValue(1)
self.fill_model_params(prefix, dgroup.prepeaks.fit_details.params)
self.fill_form(dgroup)
self.fitmodel_btn.Enable()
# self.fitallmodel_btn.Enable()
i1, i2 = self.get_xranges(dgroup.energy)
dgroup.yfit = dgroup.xfit = 0.0*dgroup.energy[i1:i2]
# self.plot_choice.SetStringSelection(PLOT_BASELINE)
self.onPlot(baseline_only=True)
def fill_model_params(self, prefix, params):
comp = self.fit_components[prefix]
parwids = comp.parwids
for pname, par in params.items():
pname = prefix + pname
if pname in parwids:
wids = parwids[pname]
if wids.minval is not None:
wids.minval.SetValue(par.min)
if wids.maxval is not None:
wids.maxval.SetValue(par.max)
wids.value.SetValue(par.value)
varstr = 'vary' if par.vary else 'fix'
if par.expr is not None:
varstr = 'constrain'
if wids.vary is not None:
wids.vary.SetStringSelection(varstr)
def onPlotModel(self, evt=None):
dgroup = self.controller.get_group()
g = self.build_fitmodel(dgroup)
self.onPlot(show_init=True)
def onPlot(self, evt=None, baseline_only=False, show_init=False):
opts = self.read_form()
dgroup = self.controller.get_group()
opts['group'] = opts['gname']
self.larch_eval(COMMANDS['prepeaks_setup'].format(**opts))
cmd = "plot_prepeaks_fit"
args = ['{gname}']
if baseline_only:
cmd = "plot_prepeaks_baseline"
else:
args.append("show_init=%s" % (show_init))
cmd = "%s(%s)" % (cmd, ', '.join(args))
self.larch_eval(cmd.format(**opts))
def addModel(self, event=None, model=None, prefix=None, isbkg=False):
if model is None and event is not None:
model = event.GetString()
if model is None or model.startswith('<'):
return
self.models_peaks.SetSelection(0)
self.models_other.SetSelection(0)
if prefix is None:
p = model[:5].lower()
curmodels = ["%s%i_" % (p, 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)
title = prefix[:-1]
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:
if model in ModelFuncs:
mclass = getattr(lm_models, ModelFuncs[model])
else:
mclass = getattr(lm_models, model+'Model')
minst = mclass(prefix=prefix)
panel = GridPanel(self.mod_nb, ncols=2, nrows=5, 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 in Fit?', size=(100, -1))
bkgbox = Check(panel, default=False, label='Is Baseline?', size=(125, -1))
if isbkg:
bkgbox.SetValue(1)
delbtn = Button(panel, 'Delete This Component', size=(200, -1),
action=partial(self.onDeleteComponent, prefix=prefix))
pick2msg = SimpleText(panel, " ", size=(125, -1))
pick2btn = Button(panel, 'Pick Values from Plotted Data', size=(200, -1),
action=partial(self.onPick2Points, prefix=prefix))
# SetTip(mname, 'Label for the model component')
SetTip(usebox, 'Use this component in fit?')
SetTip(bkgbox, 'Label this component as "background" when plotting?')
SetTip(delbtn, 'Delete this model component')
SetTip(pick2btn, 'Select X range on Plot to Guess Initial Values')
panel.Add(SLabel(label, size=(275, -1), colour='#0000AA'),
dcol=4, style=wx.ALIGN_LEFT, newrow=True)
panel.Add(usebox, dcol=2)
panel.Add(bkgbox, dcol=1, style=RIGHT)
panel.Add(pick2btn, dcol=2, style=wx.ALIGN_LEFT, newrow=True)
panel.Add(pick2msg, dcol=3, style=wx.ALIGN_RIGHT)
panel.Add(delbtn, dcol=2, style=wx.ALIGN_RIGHT)
# panel.Add(HLine(panel, size=(150, 3)), dcol=4, style=wx.ALIGN_CENTER)
panel.Add(SLabel("Parameter "), style=wx.ALIGN_LEFT, newrow=True)
panel.AddMany((SLabel(" Value"), SLabel(" Type"), SLabel(' Bounds'),
SLabel(" Min", size=(60, -1)),
SLabel(" Max", size=(60, -1)), 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=100, expr_size=150,
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.bounds,
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=100, expr_size=400,
float_size=80, prefix=prefix,
widgets=('name', 'value', 'expr'))
parwids[par.name] = pwids
panel.Add(pwids.name, newrow=True)
panel.Add(pwids.value)
panel.Add(pwids.expr, dcol=5, style=wx.ALIGN_RIGHT)
pwids.value.Disable()
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, bkgbox=bkgbox)
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))
self.fitmodel_btn.Enable()
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)
if len(self.fit_components) < 1:
self.fitmodel_btn.Disable()
# 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(win=1)
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.xdat, dgroup.ydat
i0 = index_of(dgroup.xdat, xmin)
i1 = index_of(dgroup.xdat, xmax)
x, y = dgroup.xdat[i0:i1+1], dgroup.ydat[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.xdat)
plotframe = self.controller.get_display(win=1)
plotframe.cursor_hist = []
plotframe.oplot(dgroup.xdat, 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(win=1)
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 onLoadFitResult(self, event=None):
dlg = wx.FileDialog(self, message="Load Saved File Model",
wildcard=ModelWcards, style=wx.FD_OPEN)
rfile = None
if dlg.ShowModal() == wx.ID_OK:
rfile = dlg.GetPath()
dlg.Destroy()
if rfile is None:
return
self.larch_eval("# peakmodel = lm_load_modelresult('%s')" %rfile)
result = load_modelresult(str(rfile))
for prefix in list(self.fit_components.keys()):
self.onDeleteComponent(self, prefix=prefix)
for comp in result.model.components:
isbkg = comp.prefix in result.user_options['bkg_components']
self.addModel(model=comp.func.__name__,
prefix=comp.prefix, isbkg=isbkg)
for comp in result.model.components:
parwids = self.fit_components[comp.prefix].parwids
for pname, par in result.params.items():
if pname in parwids:
wids = parwids[pname]
if wids.minval is not None:
wids.minval.SetValue(par.min)
if wids.maxval is not None:
wids.maxval.SetValue(par.max)
val = result.init_values.get(pname, par.value)
wids.value.SetValue(val)
self.fill_form(result.user_options)
def onSelPoint(self, evt=None, opt='__', relative_e0=False, 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 not None:
if relative_e0 and 'e0' in self.wids:
_x -= self.wids['e0'].GetValue()
self.wids[opt].SetValue(_x)
def get_xranges(self, x):
opts = self.read_form()
dgroup = self.controller.get_group()
en_eps = min(np.diff(dgroup.energy)) / 5.
i1 = index_of(x, opts['emin'] + en_eps)
i2 = index_of(x, opts['emax'] + en_eps) + 1
return i1, i2
def build_fitmodel(self, dgroup):
""" use fit components to build model"""
# self.summary = {'components': [], 'options': {}}
peaks = []
cmds = ["## set up pre-edge peak parameters", "peakpars = Parameters()"]
modcmds = ["## define pre-edge peak model"]
modop = " ="
opts = self.read_form()
opts['group'] = opts['gname']
self.larch_eval(COMMANDS['prepeaks_setup'].format(**opts))
for comp in self.fit_components.values():
_cen, _amp = None, None
if comp.usebox is not None and comp.usebox.IsChecked():
for parwids in comp.parwids.values():
this = parwids.param
pargs = ["'%s'" % this.name, 'value=%f' % (this.value),
'min=%f' % (this.min), 'max=%f' % (this.max)]
if this.expr is not None:
pargs.append("expr='%s'" % (this.expr))
elif not this.vary:
pargs.pop()
pargs.pop()
pargs.append("vary=False")
cmds.append("peakpars.add(%s)" % (', '.join(pargs)))
if this.name.endswith('_center'):
_cen = this.name
elif parwids.param.name.endswith('_amplitude'):
_amp = this.name
compargs = ["%s='%s'" % (k,v) for k,v in comp.mclass_kws.items()]
modcmds.append("peakmodel %s %s(%s)" % (modop, comp.mclass.__name__,
', '.join(compargs)))
modop = "+="
if not comp.bkgbox.IsChecked() and _cen is not None and _amp is not None:
peaks.append((_amp, _cen))
if len(peaks) > 0:
denom = '+'.join([p[0] for p in peaks])
numer = '+'.join(["%s*%s "% p for p in peaks])
cmds.append("peakpars.add('fit_centroid', expr='(%s)/(%s)')" % (numer, denom))
cmds.extend(modcmds)
cmds.append(COMMANDS['prepfit'].format(group=dgroup.groupname,
user_opts=repr(opts)))
self.larch_eval("\n".join(cmds))
def onFitSelected(self, event=None):
dgroup = self.controller.get_group()
self.build_fitmodel(dgroup)
def onFitModel(self, event=None):
dgroup = self.controller.get_group()
if dgroup is None:
return
self.build_fitmodel(dgroup)
opts = self.read_form()
dgroup = self.controller.get_group()
opts['group'] = opts['gname']
self.larch_eval(COMMANDS['prepeaks_setup'].format(**opts))
ppeaks = dgroup.prepeaks
# add bkg_component to saved user options
bkg_comps = []
for label, comp in self.fit_components.items():
if comp.bkgbox.IsChecked():
bkg_comps.append(label)
opts['bkg_components'] = bkg_comps
imin, imax = self.get_xranges(dgroup.xdat)
cmds = ["## do peak fit: "]
yerr_type = 'set_yerr_const'
yerr = getattr(dgroup, 'yerr', None)
if yerr is None:
if hasattr(dgroup, 'norm_std'):
cmds.append("{group}.yerr = {group}.norm_std")
yerr_type = 'set_yerr_array'
elif hasattr(dgroup, 'mu_std'):
cmds.append("{group}.yerr = {group}.mu_std/(1.e-15+{group}.edge_step)")
yerr_type = 'set_yerr_array'
else:
cmds.append("{group}.yerr = 1")
elif isinstance(dgroup.yerr, np.ndarray):
yerr_type = 'set_yerr_array'
cmds.extend([COMMANDS[yerr_type], COMMANDS['dofit']])
cmd = '\n'.join(cmds)
self.larch_eval(cmd.format(group=dgroup.groupname,
imin=imin, imax=imax,
user_opts=repr(opts)))
self.autosave_modelresult(self.larch_get("peakresult"))
self.onPlot()
self.show_subframe('prepeak_result_frame', FitResultFrame,
datagroup=dgroup, peakframe=self)
self.subframes['prepeak_result_frame'].show_results()
def update_start_values(self, params):
"""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 params.items():
if pname in allparwids:
allparwids[pname].value.SetValue(par.value)
def autosave_modelresult(self, result, fname=None):
"""autosave model result to user larch folder"""
confdir = os.path.join(site_config.usr_larchdir, 'xas_viewer')
if not os.path.exists(confdir):
try:
os.makedirs(confdir)
except OSError:
print("Warning: cannot create XAS_Viewer user folder")
return
if not HAS_MODELSAVE:
print("Warning: cannot save model results: upgrade lmfit")
return
if fname is None:
fname = 'autosave.fitmodel'
save_modelresult(result, os.path.join(confdir, fname))
class XASFrame(wx.Frame):
_about = """Larch XAS GUI: XAS Visualization and Analysis
Matt Newville <newville @ cars.uchicago.edu>
"""
def __init__(self, parent=None, _larch=None, **kws):
wx.Frame.__init__(self,
parent,
-1,
size=XASVIEW_SIZE,
style=FRAMESTYLE)
self.last_array_sel = {}
self.paths2read = []
title = "Larch XAS GUI: XAS Visualization and Analysis"
self.larch_buffer = parent
if not isinstance(parent, LarchFrame):
self.larch_buffer = LarchFrame(_larch=_larch)
self.larch_buffer.Show()
self.larch_buffer.Raise()
self.larch = self.larch_buffer.larchshell
self.larch.symtable._sys.xas_viewer = Group()
self.controller = XASController(wxparent=self, _larch=self.larch)
self.current_filename = None
self.subframes = {}
self.plotframe = None
self.SetTitle(title)
self.SetSize(XASVIEW_SIZE)
self.SetFont(Font(FONTSIZE))
self.larch_buffer.Hide()
self.createMainPanel()
self.createMenus()
self.statusbar = self.CreateStatusBar(2, 0)
self.statusbar.SetStatusWidths([-3, -1])
statusbar_fields = ["Initializing....", " "]
for i in range(len(statusbar_fields)):
self.statusbar.SetStatusText(statusbar_fields[i], i)
def createMainPanel(self):
display0 = wx.Display(0)
client_area = display0.ClientArea
xmin, ymin, xmax, ymax = client_area
xpos = int((xmax - xmin) * 0.02) + xmin
ypos = int((ymax - ymin) * 0.04) + ymin
self.SetPosition((xpos, ypos))
splitter = wx.SplitterWindow(self, style=wx.SP_LIVE_UPDATE)
splitter.SetMinimumPaneSize(250)
leftpanel = wx.Panel(splitter)
ltop = wx.Panel(leftpanel)
def Btn(msg, x, act):
b = Button(ltop, msg, size=(x, 30), action=act)
b.SetFont(Font(FONTSIZE))
return b
sel_none = Btn('Select None', 120, self.onSelNone)
sel_all = Btn('Select All', 120, self.onSelAll)
self.controller.filelist = FileCheckList(
leftpanel,
# main=self,
select_action=self.ShowFile,
remove_action=self.RemoveFile)
tsizer = wx.BoxSizer(wx.HORIZONTAL)
tsizer.Add(sel_all, 1, LCEN | wx.GROW, 1)
tsizer.Add(sel_none, 1, LCEN | wx.GROW, 1)
pack(ltop, tsizer)
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add(ltop, 0, LCEN | wx.GROW, 1)
sizer.Add(self.controller.filelist, 1, LCEN | wx.GROW | wx.ALL, 1)
pack(leftpanel, sizer)
# right hand side
panel = wx.Panel(splitter)
sizer = wx.BoxSizer(wx.VERTICAL)
self.title = SimpleText(panel, 'initializing...', size=(300, -1))
self.title.SetFont(Font(FONTSIZE + 1))
ir = 0
sizer.Add(self.title, 0, LCEN | wx.GROW | wx.ALL, 1)
self.nb = flat_nb.FlatNotebook(panel, -1, agwStyle=FNB_STYLE)
self.nb.SetTabAreaColour(wx.Colour(250, 250, 250))
self.nb.SetActiveTabColour(wx.Colour(254, 254, 195))
self.nb.SetNonActiveTabTextColour(wx.Colour(10, 10, 128))
self.nb.SetActiveTabTextColour(wx.Colour(128, 0, 0))
self.nb_panels = []
for name, creator in NB_PANELS:
_panel = creator(parent=self, controller=self.controller)
self.nb.AddPage(_panel, " %s " % name, True)
self.nb_panels.append(_panel)
sizer.Add(self.nb, 1, LCEN | wx.EXPAND, 2)
self.nb.Bind(wx.EVT_NOTEBOOK_PAGE_CHANGED, self.onNBChanged)
self.nb.SetSelection(0)
pack(panel, sizer)
splitter.SplitVertically(leftpanel, panel, 1)
wx.CallAfter(self.init_larch)
def onNBChanged(self, event=None):
idx = self.nb.GetSelection()
pan = self.nb_panels[idx]
callback = getattr(pan, 'onPanelExposed', None)
if callable(callback):
callback()
def onSelAll(self, event=None):
self.controller.filelist.SetCheckedStrings(
self.controller.file_groups.keys())
def onSelNone(self, event=None):
self.controller.filelist.SetCheckedStrings([])
def init_larch(self):
self.SetStatusText('initializing Larch')
self.title.SetLabel('')
self.controller.init_larch()
plotframe = self.controller.get_display(stacked=False)
xpos, ypos = self.GetPosition()
xsiz, ysiz = self.GetSize()
plotframe.SetPosition((xpos + xsiz + 5, ypos))
plotframe.SetSize((ysiz, ysiz))
self.SetStatusText('ready')
self.Raise()
def write_message(self, s, panel=0):
"""write a message to the Status Bar"""
self.SetStatusText(s, panel)
def RemoveFile(self, fname=None, **kws):
if fname is not None:
s = str(fname)
if s in self.controller.file_groups:
group = self.controller.file_groups.pop(s)
def ShowFile(self,
evt=None,
groupname=None,
process=True,
plot=True,
**kws):
filename = None
if evt is not None:
filename = str(evt.GetString())
if groupname is None and filename is not None:
groupname = self.controller.file_groups[filename]
if not hasattr(self.larch.symtable, groupname):
return
dgroup = self.controller.get_group(groupname)
if filename is None:
filename = dgroup.filename
self.title.SetLabel(filename)
self.current_filename = filename
self.controller.group = dgroup
self.controller.groupname = groupname
cur_panel = self.nb_panels[self.nb.GetSelection()]
if process:
cur_panel.fill_form(dgroup=dgroup)
cur_panel.process(dgroup=dgroup)
if plot and hasattr(cur_panel, 'plot'):
cur_panel.plot(dgroup=dgroup)
def createMenus(self):
# ppnl = self.plotpanel
self.menubar = wx.MenuBar()
#
fmenu = wx.Menu()
group_menu = wx.Menu()
data_menu = wx.Menu()
ppeak_menu = wx.Menu()
m = {}
MenuItem(self, fmenu, "&Open Data File\tCtrl+O", "Open Data File",
self.onReadDialog)
MenuItem(self, fmenu, "&Save Project\tCtrl+S",
"Save Session to Project File", self.onSaveProject)
MenuItem(self, fmenu, "Export Selected Groups to Athena Project",
"Export Selected Groups to Athena Project",
self.onExportAthena)
MenuItem(self, fmenu, "Export Selected Groups to CSV",
"Export Selected Groups to CSV", self.onExportCSV)
fmenu.AppendSeparator()
MenuItem(self, fmenu, 'Show Larch Buffer\tCtrl+L',
'Show Larch Programming Buffer', self.onShowLarchBuffer)
MenuItem(self, fmenu, 'Save Larch Script of History\tCtrl+H',
'Save Session History as Larch Script',
self.onSaveLarchHistory)
if WX_DEBUG:
MenuItem(self, fmenu, "&Inspect \tCtrl+J", " wx inspection tool ",
self.showInspectionTool)
MenuItem(self, fmenu, "&Quit\tCtrl+Q", "Quit program", self.onClose)
MenuItem(self, group_menu, "Copy This Group", "Copy This Group",
self.onCopyGroup)
MenuItem(self, group_menu, "Rename This Group", "Rename This Group",
self.onRenameGroup)
MenuItem(self, group_menu, "Remove Selected Groups",
"Remove Selected Group", self.onRemoveGroups)
MenuItem(self, group_menu, "Merge Selected Groups",
"Merge Selected Groups", self.onMergeData)
MenuItem(self, data_menu, "Deglitch Data", "Deglitch Data",
self.onDeglitchData)
MenuItem(self, data_menu, "Recalibrate Energy", "Recalibrate Energy",
self.onEnergyCalibrateData)
MenuItem(self, data_menu, "Smooth Data", "Smooth Data",
self.onSmoothData)
MenuItem(self, data_menu, "Rebin Data", "Rebin Data", self.onRebinData)
MenuItem(self, data_menu, "Deconvolve Data", "Deconvolution of Data",
self.onDeconvolveData)
MenuItem(self, data_menu, "Correct Over-absorption",
"Correct Over-absorption", self.onCorrectOverAbsorptionData)
MenuItem(self, ppeak_menu, "&Read Fit Model\tCtrl+R",
"Read Fit Model from File", self.onLoadFitResult)
fsave = MenuItem(self, ppeak_menu, "Save Fit Model",
"Save Fit Model to File", self.onSaveFitResult)
fexport = MenuItem(self, ppeak_menu, "Export Data and Fit",
"Export Data and Fit", self.onExportFitResult)
self.afterfit_menus = (fsave, fexport)
for m in self.afterfit_menus:
m.Enable(False)
self.menubar.Append(fmenu, "&File")
self.menubar.Append(group_menu, "Groups")
self.menubar.Append(data_menu, "Data")
self.menubar.Append(ppeak_menu, "PreEdgePeaks")
self.SetMenuBar(self.menubar)
self.Bind(wx.EVT_CLOSE, self.onClose)
def onShowLarchBuffer(self, evt=None):
if self.larch_buffer is None:
self.larch_buffer = LarchFrame(_larch=self.larch)
self.larch_buffer.Show()
self.larch_buffer.Raise()
def onSaveLarchHistory(self, evt=None):
wildcard = 'Larch file (*.lar)|*.lar|All files (*.*)|*.*'
path = FileSave(self,
message='Save Session History as Larch Script',
wildcard=wildcard,
default_file='xas_viewer_history.lar')
if path is not None:
self.larch._larch.input.history.save(path, session_only=True)
self.SetStatusText("Wrote %s" % path, 0)
def onExportCSV(self, evt=None):
group_ids = self.controller.filelist.GetCheckedStrings()
savegroups = []
groupnames = []
for checked in group_ids:
groupname = self.controller.file_groups[str(checked)]
dgroup = self.controller.get_group(groupname)
savegroups.append(dgroup)
groupnames.append(groupname)
if len(savegroups) < 1:
Popup(self, "No files selected to export to CSV",
"No files selected")
return
deffile = "%s_%i.csv" % (groupname, len(groupnames))
wcards = 'CSV Files (*.csv)|*.cvs|All files (*.*)|*.*'
outfile = FileSave(self,
'Export Selected Groups to CSV File',
default_file=deffile,
wildcard=wcards)
if outfile is None:
return
groups2csv(savegroups,
outfile,
x='energy',
y='norm',
_larch=self.larch)
def onExportAthena(self, evt=None):
groups = []
for checked in self.controller.filelist.GetCheckedStrings():
groups.append(self.controller.file_groups[str(checked)])
if len(groups) < 1:
Popup(self, "No files selected to export to Athena",
"No files selected")
return
self.save_athena_project(groups[0], groups, prompt=True)
def onSaveProject(self, evt=None):
groups = [gname for gname in self.controller.file_groups]
if len(groups) < 1:
Popup(self, "No files selected to export to Athena",
"No files selected")
return
self.save_athena_project(groups[0], groups, prompt=True)
def save_athena_project(self, filename, grouplist, prompt=True):
if len(grouplist) < 1:
return
savegroups = [self.controller.get_group(gname) for gname in grouplist]
deffile = "%s_%i.prj" % (filename, len(grouplist))
wcards = 'Athena Projects (*.prj)|*.prj|All files (*.*)|*.*'
outfile = FileSave(self,
'Save Groups to Athena Project File',
default_file=deffile,
wildcard=wcards)
if outfile is None:
return
aprj = AthenaProject(filename=outfile, _larch=self.larch)
for label, grp in zip(grouplist, savegroups):
aprj.add_group(grp, label=label)
aprj.save(use_gzip=True)
def onConfigDataProcessing(self, event=None):
pass
def onNewGroup(self, datagroup):
"""
install and display a new group, as from 'copy / modify'
Note: this is a group object, not the groupname or filename
"""
dgroup = datagroup
self.install_group(dgroup.groupname, dgroup.filename, overwrite=False)
self.ShowFile(groupname=dgroup.groupname)
def onCopyGroup(self, event=None):
fname = self.current_filename
if fname is None:
fname = self.controller.filelist.GetStringSelection()
ngroup = self.controller.copy_group(fname)
self.onNewGroup(ngroup)
def onRenameGroup(self, event=None):
fname = self.current_filename = self.controller.filelist.GetStringSelection(
)
if fname is None:
return
dlg = RenameDialog(self, fname)
res = dlg.GetResponse()
dlg.Destroy()
if res.ok:
selected = []
for checked in self.controller.filelist.GetCheckedStrings():
selected.append(str(checked))
if self.current_filename in selected:
selected.remove(self.current_filename)
selected.append(res.newname)
groupname = self.controller.file_groups.pop(fname)
self.controller.file_groups[res.newname] = groupname
self.controller.filelist.rename_item(self.current_filename,
res.newname)
dgroup = self.controller.get_group(groupname)
dgroup.filename = self.current_filename = res.newname
self.controller.filelist.SetCheckedStrings(selected)
self.controller.filelist.SetStringSelection(res.newname)
def onRemoveGroups(self, event=None):
groups = []
for checked in self.controller.filelist.GetCheckedStrings():
groups.append(str(checked))
if len(groups) < 1:
return
dlg = RemoveDialog(self, groups)
res = dlg.GetResponse()
dlg.Destroy()
if res.ok:
filelist = self.controller.filelist
all_fnames = filelist.GetItems()
for fname in groups:
gname = self.controller.file_groups.pop(fname)
delattr(self.controller.symtable, gname)
all_fnames.remove(fname)
filelist.Clear()
for name in all_fnames:
filelist.Append(name)
def onMergeData(self, event=None):
groups = []
for checked in self.controller.filelist.GetCheckedStrings():
groups.append(self.controller.file_groups[str(checked)])
if len(groups) < 1:
return
outgroup = unique_name('merge', self.controller.file_groups)
dlg = MergeDialog(self, groups, outgroup=outgroup)
res = dlg.GetResponse()
dlg.Destroy()
if res.ok:
fname = res.group
gname = fix_varname(res.group.lower())
yname = 'norm' if res.ynorm else 'mu'
self.controller.merge_groups(groups,
master=res.master,
yarray=yname,
outgroup=gname)
self.install_group(gname, fname, overwrite=False)
self.controller.filelist.SetStringSelection(fname)
def onDeglitchData(self, event=None):
DeglitchDialog(self, self.controller).Show()
def onSmoothData(self, event=None):
SmoothDataDialog(self, self.controller).Show()
def onRebinData(self, event=None):
RebinDataDialog(self, self.controller).Show()
def onCorrectOverAbsorptionData(self, event=None):
OverAbsorptionDialog(self, self.controller).Show()
def onEnergyCalibrateData(self, event=None):
EnergyCalibrateDialog(self, self.controller).Show()
def onDeconvolveData(self, event=None):
DeconvolutionDialog(self, self.controller).Show()
def onConfigDataFitting(self, event=None):
pass
def showInspectionTool(self, event=None):
app = wx.GetApp()
app.ShowInspectionTool()
def onAbout(self, evt):
dlg = wx.MessageDialog(self, self._about, "About Larch XAS GUI",
wx.OK | wx.ICON_INFORMATION)
dlg.ShowModal()
dlg.Destroy()
def onClose(self, event):
dlg = QuitDialog(self)
res = dlg.GetResponse()
dlg.Destroy()
if not res.ok:
return
if res.save:
groups = [gname for gname in self.controller.file_groups]
if len(groups) > 0:
self.save_athena_project(groups[0], groups, prompt=True)
self.controller.save_config()
self.controller.get_display().Destroy()
if self.larch_buffer is not None:
try:
self.larch_buffer.Destroy()
except:
pass
time.sleep(0.05)
for nam in dir(self.larch.symtable._plotter):
obj = getattr(self.larch.symtable._plotter, nam)
time.sleep(0.05)
try:
obj.Destroy()
except:
pass
for name, wid in self.subframes.items():
if wid is not None:
try:
wid.Destroy()
except:
pass
for nam in dir(self.larch.symtable._sys.wx):
obj = getattr(self.larch.symtable._sys.wx, nam)
self.Destroy()
def show_subframe(self, name, frameclass, **opts):
shown = False
if name in self.subframes:
try:
self.subframes[name].Raise()
shown = True
except:
del self.subframes[name]
if not shown:
self.subframes[name] = frameclass(self, **opts)
def onSelectColumns(self, event=None):
dgroup = self.controller.get_group()
self.show_subframe('readfile',
ColumnDataFileFrame,
group=dgroup.raw,
last_array_sel=self.last_array_sel,
_larch=self.larch,
read_ok_cb=partial(self.onRead_OK, overwrite=True))
def onLoadFitResult(self, event=None):
self.nb.SetSelection(1)
self.nb_panels[1].onLoadFitResult(event=event)
def onSaveFitResult(self, event=None):
self.nb_panels[1].onSaveFitResult(event=event)
def onExportFitResult(self, event=None):
self.nb_panels[1].onExportFitResult(event=event)
def onReadDialog(self, event=None):
dlg = wx.FileDialog(self,
message="Read Data File",
defaultDir=os.getcwd(),
wildcard=FILE_WILDCARDS,
style=wx.FD_OPEN | wx.FD_MULTIPLE)
self.paths2read = []
if dlg.ShowModal() == wx.ID_OK:
self.paths2read = dlg.GetPaths()
dlg.Destroy()
if len(self.paths2read) < 1:
return
path = self.paths2read.pop(0)
path = path.replace('\\', '/')
do_read = True
if path in self.controller.file_groups:
do_read = (wx.ID_YES == Popup(self, "Re-read file '%s'?" % path,
'Re-read file?'))
if do_read:
self.onRead(path)
def onRead(self, path):
filedir, filename = os.path.split(path)
if self.controller.get_config('chdir_on_fileopen'):
os.chdir(filedir)
self.controller.set_workdir()
# check for athena projects
if is_athena_project(path):
kwargs = dict(filename=path,
_larch=self.controller.larch,
read_ok_cb=self.onReadAthenaProject_OK)
self.show_subframe('athena_import', AthenaImporter, **kwargs)
else:
kwargs = dict(filename=path,
_larch=self.larch_buffer.larchshell,
last_array_sel=self.last_array_sel,
read_ok_cb=self.onRead_OK)
self.show_subframe('readfile', ColumnDataFileFrame, **kwargs)
def onReadAthenaProject_OK(self, path, namelist):
"""read groups from a list of groups from an athena project file"""
self.larch.eval(
"_prj = read_athena('{path:s}', do_fft=False, do_bkg=False)".
format(path=path))
dgroup = None
script = "{group:s} = extract_athenagroup(_prj.{prjgroup:s})"
for gname in namelist:
this = getattr(self.larch.symtable._prj, gname)
gid = str(getattr(this, 'athena_id', gname))
self.larch.eval(script.format(group=gid, prjgroup=gname))
dgroup = self.install_group(gid, gname, process=True, plot=False)
self.larch.eval("del _prj")
def onRead_OK(self,
script,
path,
groupname=None,
array_sel=None,
overwrite=False):
""" called when column data has been selected and is ready to be used
overwrite: whether to overwrite the current datagroup, as when
editing a datagroup
"""
abort_read = False
filedir, filename = os.path.split(path)
if not overwrite and hasattr(self.larch.symtable, groupname):
newname = file2groupname(filename, symtable=self.larch.symtable)
msg = """Warning: groupname '%s' already used.
Will use groupname '%s' instead """ % (groupname, newname)
dlg = wx.MessageDialog(self, msg, 'Warning', wx.OK | wx.CANCEL)
abort_read = (wx.ID_OK != dlg.ShowModal())
dlg.Destroy()
groupname = newname
if abort_read:
return
self.larch.eval(script.format(group=groupname, path=path))
if array_sel is not None:
self.last_array_sel = array_sel
self.install_group(groupname, filename, overwrite=overwrite)
for path in self.paths2read:
path = path.replace('\\', '/')
filedir, filename = os.path.split(path)
gname = file2groupname(filename, symtable=self.larch.symtable)
self.larch.eval(script.format(group=gname, path=path))
self.install_group(gname, filename, overwrite=True)
def install_group(self,
groupname,
filename,
overwrite=False,
process=True,
plot=True):
"""add groupname / filename to list of available data groups"""
thisgroup = getattr(self.larch.symtable, groupname)
thisgroup.groupname = groupname
thisgroup.filename = filename
datatype = getattr(thisgroup, 'datatype', 'raw')
# file /group may already exist in list
if filename in self.controller.file_groups and not overwrite:
for i in range(1, 101):
ftest = "%s (%i)" % (filename, i)
if ftest not in self.controller.file_groups:
filename = ftest
break
if filename not in self.controller.file_groups:
self.controller.filelist.Append(filename)
self.controller.file_groups[filename] = groupname
self.nb.SetSelection(0)
self.ShowFile(groupname=groupname, process=process, plot=plot)
self.controller.filelist.SetStringSelection(filename)
return thisgroup
class XASFrame(wx.Frame):
_about = """Larch XAS GUI: XAS Visualization and Analysis
Matt Newville <newville @ cars.uchicago.edu>
"""
def __init__(self, parent=None, _larch=None, filename=None, **kws):
wx.Frame.__init__(self,
parent,
-1,
size=XASVIEW_SIZE,
style=FRAMESTYLE)
self.last_array_sel = {}
self.paths2read = []
title = "Larch XAS GUI: XAS Visualization and Analysis"
self.larch_buffer = parent
if not isinstance(parent, LarchFrame):
self.larch_buffer = LarchFrame(_larch=_larch, is_standalone=False)
self.larch_buffer.Show()
self.larch_buffer.Raise()
self.larch = self.larch_buffer.larchshell
self.larch.symtable._sys.xas_viewer = Group()
self.controller = XASController(wxparent=self, _larch=self.larch)
self.subframes = {}
self.plotframe = None
self.SetTitle(title)
self.SetSize(XASVIEW_SIZE)
self.SetFont(Font(FONTSIZE))
self.larch_buffer.Hide()
self.createMainPanel()
self.createMenus()
self.statusbar = self.CreateStatusBar(2, style=wx.STB_DEFAULT_STYLE)
self.statusbar.SetStatusWidths([-3, -1])
statusbar_fields = [" ", "initializing...."]
for i in range(len(statusbar_fields)):
self.statusbar.SetStatusText(statusbar_fields[i], i)
self.current_filename = filename
self.Show()
if filename is not None:
wx.CallAfter(self.onRead, filename)
def createMainPanel(self):
display0 = wx.Display(0)
client_area = display0.ClientArea
xmin, ymin, xmax, ymax = client_area
xpos = int((xmax - xmin) * 0.02) + xmin
ypos = int((ymax - ymin) * 0.04) + ymin
self.SetPosition((xpos, ypos))
splitter = wx.SplitterWindow(self, style=wx.SP_LIVE_UPDATE)
splitter.SetMinimumPaneSize(250)
leftpanel = wx.Panel(splitter)
ltop = wx.Panel(leftpanel)
def Btn(msg, x, act):
b = Button(ltop, msg, size=(x, 30), action=act)
b.SetFont(Font(FONTSIZE))
return b
sel_none = Btn('Select None', 120, self.onSelNone)
sel_all = Btn('Select All', 120, self.onSelAll)
self.controller.filelist = FileCheckList(leftpanel,
select_action=self.ShowFile,
remove_action=self.RemoveFile)
tsizer = wx.BoxSizer(wx.HORIZONTAL)
tsizer.Add(sel_all, 1, LEFT | wx.GROW, 1)
tsizer.Add(sel_none, 1, LEFT | wx.GROW, 1)
pack(ltop, tsizer)
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add(ltop, 0, LEFT | wx.GROW, 1)
sizer.Add(self.controller.filelist, 1, LEFT | wx.GROW | wx.ALL, 1)
pack(leftpanel, sizer)
# right hand side
panel = wx.Panel(splitter)
sizer = wx.BoxSizer(wx.VERTICAL)
self.title = SimpleText(panel, 'initializing...', size=(300, -1))
self.title.SetFont(Font(FONTSIZE + 2))
ir = 0
sizer.Add(self.title, 0, LEFT | wx.GROW | wx.ALL, 1)
self.nb = flatnotebook(panel,
NB_PANELS,
panelkws=dict(controller=self.controller),
on_change=self.onNBChanged)
sizer.Add(self.nb, 1, LEFT | wx.EXPAND, 2)
pack(panel, sizer)
splitter.SplitVertically(leftpanel, panel, 1)
wx.CallAfter(self.init_larch)
def onNBChanged(self, event=None):
callback = getattr(self.nb.GetCurrentPage(), 'onPanelExposed', None)
if callable(callback):
callback()
def onSelAll(self, event=None):
self.controller.filelist.select_all()
def onSelNone(self, event=None):
self.controller.filelist.select_none()
def init_larch(self):
self.SetStatusText('initializing Larch', 1)
self.title.SetLabel('')
self.controller.init_larch()
plotframe = self.controller.get_display(stacked=False)
xpos, ypos = self.GetPosition()
xsiz, ysiz = self.GetSize()
plotframe.SetPosition((xpos + xsiz + 5, ypos))
plotframe.SetSize((600, 650))
self.SetStatusText('ready', 1)
self.Raise()
def write_message(self, msg, panel=0):
"""write a message to the Status Bar"""
self.statusbar.SetStatusText(msg, panel)
def RemoveFile(self, fname=None, **kws):
if fname is not None:
s = str(fname)
if s in self.controller.file_groups:
group = self.controller.file_groups.pop(s)
def ShowFile(self,
evt=None,
groupname=None,
process=True,
plot=True,
**kws):
filename = None
if evt is not None:
filename = str(evt.GetString())
if groupname is None and filename is not None:
groupname = self.controller.file_groups[filename]
if not hasattr(self.larch.symtable, groupname):
return
dgroup = self.controller.get_group(groupname)
if dgroup is None:
return
if filename is None:
filename = dgroup.filename
self.title.SetLabel(filename)
self.current_filename = filename
self.controller.group = dgroup
self.controller.groupname = groupname
cur_panel = self.nb.GetCurrentPage()
if process:
cur_panel.fill_form(dgroup)
cur_panel.skip_process = True
cur_panel.process(dgroup=dgroup)
if plot and hasattr(cur_panel, 'plot'):
cur_panel.plot(dgroup=dgroup)
cur_panel.skip_process = False
def createMenus(self):
# ppnl = self.plotpanel
self.menubar = wx.MenuBar()
fmenu = wx.Menu()
group_menu = wx.Menu()
data_menu = wx.Menu()
# ppeak_menu = wx.Menu()
m = {}
MenuItem(self, fmenu, "&Open Data File\tCtrl+O", "Open Data File",
self.onReadDialog)
MenuItem(self, fmenu, "&Save Project\tCtrl+S",
"Save Session to Project File", self.onSaveProject)
MenuItem(self, fmenu, "Export Selected Groups to Athena Project",
"Export Selected Groups to Athena Project",
self.onExportAthena)
MenuItem(self, fmenu, "Export Selected Groups to CSV",
"Export Selected Groups to CSV", self.onExportCSV)
fmenu.AppendSeparator()
MenuItem(self, fmenu, 'Show Larch Buffer\tCtrl+L',
'Show Larch Programming Buffer', self.onShowLarchBuffer)
MenuItem(self, fmenu, 'Save Larch Script of History\tCtrl+H',
'Save Session History as Larch Script',
self.onSaveLarchHistory)
if WX_DEBUG:
MenuItem(self, fmenu, "&Inspect \tCtrl+J", " wx inspection tool ",
self.showInspectionTool)
MenuItem(self, fmenu, "&Quit\tCtrl+Q", "Quit program", self.onClose)
MenuItem(self, group_menu, "Copy This Group", "Copy This Group",
self.onCopyGroup)
MenuItem(self, group_menu, "Rename This Group", "Rename This Group",
self.onRenameGroup)
MenuItem(self, group_menu, "Remove Selected Groups",
"Remove Selected Group", self.onRemoveGroups)
group_menu.AppendSeparator()
MenuItem(self, group_menu, "Merge Selected Groups",
"Merge Selected Groups", self.onMergeData)
group_menu.AppendSeparator()
MenuItem(self, group_menu, "Freeze Selected Groups",
"Freeze Selected Groups", self.onFreezeGroups)
MenuItem(self, group_menu, "UnFreeze Selected Groups",
"UnFreeze Selected Groups", self.onUnFreezeGroups)
MenuItem(self, data_menu, "Deglitch Data", "Deglitch Data",
self.onDeglitchData)
MenuItem(self, data_menu, "Recalibrate Energy", "Recalibrate Energy",
self.onEnergyCalibrateData)
MenuItem(self, data_menu, "Smooth Data", "Smooth Data",
self.onSmoothData)
MenuItem(self, data_menu, "Rebin Data", "Rebin Data", self.onRebinData)
MenuItem(self, data_menu, "Deconvolve Data", "Deconvolution of Data",
self.onDeconvolveData)
MenuItem(self, data_menu, "Correct Over-absorption",
"Correct Over-absorption", self.onCorrectOverAbsorptionData)
MenuItem(self, data_menu, "Add and Subtract Sepctra",
"Calculations of Spectra", self.onSpectraCalc)
self.menubar.Append(fmenu, "&File")
self.menubar.Append(group_menu, "Groups")
self.menubar.Append(data_menu, "Data")
# self.menubar.Append(ppeak_menu, "PreEdgePeaks")
self.SetMenuBar(self.menubar)
self.Bind(wx.EVT_CLOSE, self.onClose)
def onShowLarchBuffer(self, evt=None):
if self.larch_buffer is None:
self.larch_buffer = LarchFrame(_larch=self.larch,
is_standalone=False)
self.larch_buffer.Show()
self.larch_buffer.Raise()
def onSaveLarchHistory(self, evt=None):
wildcard = 'Larch file (*.lar)|*.lar|All files (*.*)|*.*'
path = FileSave(self,
message='Save Session History as Larch Script',
wildcard=wildcard,
default_file='xas_viewer_history.lar')
if path is not None:
self.larch._larch.input.history.save(path, session_only=True)
self.write_message("Wrote history %s" % path, 0)
def onExportCSV(self, evt=None):
filenames = self.controller.filelist.GetCheckedStrings()
if len(filenames) < 1:
Popup(self, "No files selected to export to CSV",
"No files selected")
return
dlg = ExportCSVDialog(self, filenames)
res = dlg.GetResponse()
dlg.Destroy()
if res.ok:
savegroups = [self.controller.filename2group(res.master)]
for fname in filenames:
dgroup = self.controller.filename2group(fname)
if dgroup not in savegroups:
savegroups.append(dgroup)
groups2csv(savegroups,
res.filename,
x='energy',
y=res.yarray,
_larch=self.larch)
self.write_message("Exported CSV file %s" % (res.filename))
def onExportAthena(self, evt=None):
groups = []
for checked in self.controller.filelist.GetCheckedStrings():
groups.append(self.controller.file_groups[str(checked)])
if len(groups) < 1:
Popup(self, "No files selected to export to Athena",
"No files selected")
return
self.save_athena_project(groups[0], groups, prompt=True)
def onSaveProject(self, evt=None):
groups = [gname for gname in self.controller.file_groups]
if len(groups) < 1:
Popup(self, "No files selected to export to Athena",
"No files selected")
return
self.save_athena_project(groups[0], groups, prompt=True)
def save_athena_project(self, filename, grouplist, prompt=True):
if len(grouplist) < 1:
return
savegroups = [self.controller.get_group(gname) for gname in grouplist]
deffile = "%s_%i.prj" % (filename, len(grouplist))
wcards = 'Athena Projects (*.prj)|*.prj|All files (*.*)|*.*'
outfile = FileSave(self,
'Save Groups to Athena Project File',
default_file=deffile,
wildcard=wcards)
if outfile is None:
return
aprj = AthenaProject(filename=outfile, _larch=self.larch)
for label, grp in zip(grouplist, savegroups):
aprj.add_group(grp)
aprj.save(use_gzip=True)
self.write_message("Saved project file %s" % (outfile))
def onConfigDataProcessing(self, event=None):
pass
def onNewGroup(self, datagroup):
"""
install and display a new group, as from 'copy / modify'
Note: this is a group object, not the groupname or filename
"""
dgroup = datagroup
self.install_group(dgroup.groupname, dgroup.filename, overwrite=False)
self.ShowFile(groupname=dgroup.groupname)
def onCopyGroup(self, event=None):
fname = self.current_filename
if fname is None:
fname = self.controller.filelist.GetStringSelection()
ngroup = self.controller.copy_group(fname)
self.onNewGroup(ngroup)
def onRenameGroup(self, event=None):
fname = self.current_filename = self.controller.filelist.GetStringSelection(
)
if fname is None:
return
dlg = RenameDialog(self, fname)
res = dlg.GetResponse()
dlg.Destroy()
if res.ok:
selected = []
for checked in self.controller.filelist.GetCheckedStrings():
selected.append(str(checked))
if self.current_filename in selected:
selected.remove(self.current_filename)
selected.append(res.newname)
groupname = self.controller.file_groups.pop(fname)
self.controller.file_groups[res.newname] = groupname
self.controller.filelist.rename_item(self.current_filename,
res.newname)
dgroup = self.controller.get_group(groupname)
dgroup.filename = self.current_filename = res.newname
self.controller.filelist.SetCheckedStrings(selected)
self.controller.filelist.SetStringSelection(res.newname)
def onRemoveGroups(self, event=None):
groups = []
for checked in self.controller.filelist.GetCheckedStrings():
groups.append(str(checked))
if len(groups) < 1:
return
dlg = RemoveDialog(self, groups)
res = dlg.GetResponse()
dlg.Destroy()
if res.ok:
filelist = self.controller.filelist
all_fnames = filelist.GetItems()
for fname in groups:
gname = self.controller.file_groups.pop(fname)
delattr(self.controller.symtable, gname)
all_fnames.remove(fname)
filelist.Clear()
for name in all_fnames:
filelist.Append(name)
def onFreezeGroups(self, event=None):
self._freeze_handler(True)
def onUnFreezeGroups(self, event=None):
self._freeze_handler(False)
def _freeze_handler(self, freeze):
current_filename = self.current_filename
reproc_group = None
for fname in self.controller.filelist.GetCheckedStrings():
groupname = self.controller.file_groups[str(fname)]
dgroup = self.controller.get_group(groupname)
if fname == current_filename:
reproc_group = groupname
dgroup.is_frozen = freeze
if reproc_group is not None:
self.ShowFile(groupname=reproc_group, process=True)
def onMergeData(self, event=None):
groups = OrderedDict()
for checked in self.controller.filelist.GetCheckedStrings():
cname = str(checked)
groups[cname] = self.controller.file_groups[cname]
if len(groups) < 1:
return
outgroup = common_startstring(list(groups.keys()))
outgroup = "%s (merge %d)" % (outgroup, len(groups))
outgroup = unique_name(outgroup, self.controller.file_groups)
dlg = MergeDialog(self, list(groups.keys()), outgroup=outgroup)
res = dlg.GetResponse()
dlg.Destroy()
if res.ok:
fname = res.group
gname = fix_varname(res.group.lower())
master = self.controller.file_groups[res.master]
yname = 'norm' if res.ynorm else 'mu'
self.controller.merge_groups(list(groups.values()),
master=master,
yarray=yname,
outgroup=gname)
self.install_group(gname, fname, overwrite=False)
self.controller.filelist.SetStringSelection(fname)
def onDeglitchData(self, event=None):
DeglitchDialog(self, self.controller).Show()
def onSmoothData(self, event=None):
SmoothDataDialog(self, self.controller).Show()
def onRebinData(self, event=None):
RebinDataDialog(self, self.controller).Show()
def onCorrectOverAbsorptionData(self, event=None):
OverAbsorptionDialog(self, self.controller).Show()
def onSpectraCalc(self, event=None):
SpectraCalcDialog(self, self.controller).Show()
def onEnergyCalibrateData(self, event=None):
EnergyCalibrateDialog(self, self.controller).Show()
def onDeconvolveData(self, event=None):
DeconvolutionDialog(self, self.controller).Show()
def onConfigDataFitting(self, event=None):
pass
def showInspectionTool(self, event=None):
app = wx.GetApp()
app.ShowInspectionTool()
def onAbout(self, evt):
dlg = wx.MessageDialog(self, self._about, "About Larch XAS GUI",
wx.OK | wx.ICON_INFORMATION)
dlg.ShowModal()
dlg.Destroy()
def onClose(self, event):
dlg = QuitDialog(self)
dlg.Raise()
dlg.SetWindowStyle(wx.STAY_ON_TOP)
res = dlg.GetResponse()
dlg.Destroy()
if not res.ok:
return
if res.save:
groups = [gname for gname in self.controller.file_groups]
if len(groups) > 0:
self.save_athena_project(groups[0], groups, prompt=True)
self.controller.save_config()
wx.CallAfter(self.controller.close_all_displays)
if self.larch_buffer is not None:
wx.CallAfter(self.larch_buffer.Destroy)
for name, wid in self.subframes.items():
if hasattr(wid, 'Destroy'):
wx.CallAfter(wid.Destroy)
self.Destroy()
def show_subframe(self, name, frameclass, **opts):
shown = False
if name in self.subframes:
try:
self.subframes[name].Raise()
shown = True
except:
del self.subframes[name]
if not shown:
self.subframes[name] = frameclass(self, **opts)
def onSelectColumns(self, event=None):
dgroup = self.controller.get_group()
self.show_subframe('readfile',
ColumnDataFileFrame,
group=dgroup.raw,
last_array_sel=self.last_array_sel,
_larch=self.larch,
read_ok_cb=partial(self.onRead_OK, overwrite=True))
def onLoadFitResult(self, event=None):
pass
# print("onLoadFitResult??")
# self.nb.SetSelection(1)
# self.nb_panels[1].onLoadFitResult(event=event)
def onReadDialog(self, event=None):
dlg = wx.FileDialog(self,
message="Read Data File",
defaultDir=os.getcwd(),
wildcard=FILE_WILDCARDS,
style=wx.FD_OPEN | wx.FD_MULTIPLE)
self.paths2read = []
if dlg.ShowModal() == wx.ID_OK:
self.paths2read = dlg.GetPaths()
dlg.Destroy()
if len(self.paths2read) < 1:
return
path = self.paths2read.pop(0)
path = path.replace('\\', '/')
do_read = True
if path in self.controller.file_groups:
do_read = (wx.ID_YES == Popup(self, "Re-read file '%s'?" % path,
'Re-read file?'))
if do_read:
self.onRead(path)
def onRead(self, path):
filedir, filename = os.path.split(os.path.abspath(path))
if self.controller.get_config('chdir_on_fileopen'):
os.chdir(filedir)
self.controller.set_workdir()
# check for athena projects
if is_athena_project(path):
kwargs = dict(filename=path,
_larch=self.controller.larch,
read_ok_cb=self.onReadAthenaProject_OK)
self.show_subframe('athena_import', AthenaImporter, **kwargs)
else:
kwargs = dict(filename=path,
_larch=self.larch_buffer.larchshell,
last_array_sel=self.last_array_sel,
read_ok_cb=self.onRead_OK)
self.show_subframe('readfile', ColumnDataFileFrame, **kwargs)
def onReadAthenaProject_OK(self, path, namelist):
"""read groups from a list of groups from an athena project file"""
self.larch.eval(
"_prj = read_athena('{path:s}', do_fft=False, do_bkg=False)".
format(path=path))
dgroup = None
script = "{group:s} = extract_athenagroup(_prj.{prjgroup:s})"
cur_panel = self.nb.GetCurrentPage()
cur_panel.skip_plotting = True
for gname in namelist:
cur_panel.skip_plotting = (gname == namelist[-1])
this = getattr(self.larch.symtable._prj, gname)
gid = str(getattr(this, 'athena_id', gname))
if self.larch.symtable.has_group(gid):
count, prefix = 0, gname[:3]
while count < 1e7 and self.larch.symtable.has_group(gid):
gid = prefix + make_hashkey(length=7)
count += 1
self.larch.eval(script.format(group=gid, prjgroup=gname))
dgroup = self.install_group(gid, gname, process=True, plot=False)
self.larch.eval("del _prj")
cur_panel.skip_plotting = False
if len(namelist) > 0:
gname = self.controller.file_groups[namelist[0]]
self.ShowFile(groupname=gname, process=True, plot=True)
self.write_message("read %d datasets from %s" % (len(namelist), path))
def onRead_OK(self,
script,
path,
groupname=None,
filename=None,
array_sel=None,
overwrite=False):
""" called when column data has been selected and is ready to be used
overwrite: whether to overwrite the current datagroup, as when
editing a datagroup
"""
if groupname is None:
return
abort_read = False
filedir, real_filename = os.path.split(path)
if filename is None:
filename = real_filename
if not overwrite and hasattr(self.larch.symtable, groupname):
groupname = file2groupname(real_filename,
symtable=self.larch.symtable)
if abort_read:
return
self.larch.eval(script.format(group=groupname, path=path))
if array_sel is not None:
self.last_array_sel = array_sel
self.install_group(groupname, filename, overwrite=overwrite)
# check if rebin is needed
thisgroup = getattr(self.larch.symtable, groupname)
do_rebin = False
if thisgroup.datatype == 'xas':
try:
en = thisgroup.energy
except:
do_rebin = True
en = thisgroup.energy = thisgroup.xdat
# test for rebinning:
# too many data points
# unsorted energy data or data in angle
# too fine a step size at the end of the data range
if (len(en) > 1200 or any(np.diff(en) < 0)
or ((max(en) - min(en)) > 300 and
(np.diff(en[-50:]).mean() < 0.75))):
msg = """This dataset may need to be rebinned.
Rebin now?"""
dlg = wx.MessageDialog(self, msg, 'Warning', wx.YES | wx.NO)
do_rebin = (wx.ID_YES == dlg.ShowModal())
dlg.Destroy()
for path in self.paths2read:
path = path.replace('\\', '/')
filedir, real_filename = os.path.split(path)
gname = file2groupname(real_filename, symtable=self.larch.symtable)
self.larch.eval(script.format(group=gname, path=path))
self.install_group(gname, real_filename, overwrite=overwrite)
self.write_message("read %s" % (real_filename))
if do_rebin:
RebinDataDialog(self, self.controller).Show()
def install_group(self,
groupname,
filename,
overwrite=False,
process=True,
rebin=False,
plot=True):
"""add groupname / filename to list of available data groups"""
thisgroup = getattr(self.larch.symtable, groupname)
datatype = getattr(thisgroup, 'datatype', 'raw')
# file /group may already exist in list
if filename in self.controller.file_groups and not overwrite:
fbase, i = filename, 0
while i < 10000 and filename in self.controller.file_groups:
filename = "%s_%d" % (fbase, i)
i += 1
cmds = [
"%s.groupname = '%s'" % (groupname, groupname),
"%s.filename = '%s'" % (groupname, filename)
]
self.larch.eval('\n'.join(cmds))
self.controller.filelist.Append(filename)
self.controller.file_groups[filename] = groupname
self.nb.SetSelection(0)
self.ShowFile(groupname=groupname, process=process, plot=plot)
self.controller.filelist.SetStringSelection(filename)
return thisgroup
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 build_display(self):
panel = self.panel
wids = self.wids
self.skip_process = True
wids['fitspace'] = Choice(panel,
choices=FitSpace_Choices,
size=(250, -1))
wids['fitspace'].SetStringSelection(norm)
# wids['plotchoice'] = Choice(panel, choices=Plot_Choices,
# size=(250, -1), action=self.onPlot)
wids['method'] = Choice(panel,
choices=Regress_Choices,
size=(250, -1),
action=self.onRegressMethod)
add_text = self.add_text
opts = dict(digits=2, increment=1.0)
w_xmin = self.add_floatspin('xmin', value=defaults['xmin'], **opts)
w_xmax = self.add_floatspin('xmax', value=defaults['xmax'], **opts)
wids['alpha'] = NumericCombo(panel,
make_steps(),
fmt='%.6g',
default_val=0.01,
width=100)
wids['auto_scale_pls'] = Check(panel,
default=True,
label='auto scale?')
wids['auto_alpha'] = Check(panel, default=False, label='auto alpha?')
wids['fit_intercept'] = Check(panel,
default=True,
label='fit intercept?')
wids['save_csv'] = Button(panel,
'Save CSV File',
size=(150, -1),
action=self.onSaveCSV)
wids['load_csv'] = Button(panel,
'Load CSV File',
size=(150, -1),
action=self.onLoadCSV)
wids['save_model'] = Button(panel,
'Save Model',
size=(150, -1),
action=self.onSaveModel)
wids['save_model'].Disable()
wids['load_model'] = Button(panel,
'Load Model',
size=(150, -1),
action=self.onLoadModel)
wids['train_model'] = Button(panel,
'Train Model From These Data',
size=(275, -1),
action=self.onTrainModel)
wids['fit_group'] = Button(panel,
'Predict Variable for Selected Groups',
size=(275, -1),
action=self.onPredictGroups)
wids['fit_group'].Disable()
w_cvfolds = self.add_floatspin('cv_folds',
digits=0,
with_pin=False,
value=0,
increment=1,
min_val=-1)
w_cvreps = self.add_floatspin('cv_repeats',
digits=0,
with_pin=False,
value=0,
increment=1,
min_val=-1)
w_ncomps = self.add_floatspin('ncomps',
digits=0,
with_pin=False,
value=3,
increment=1,
min_val=1)
wids['varname'] = wx.TextCtrl(panel, -1, 'valence', size=(150, -1))
wids['stat1'] = SimpleText(panel, ' - - - ')
wids['stat2'] = SimpleText(panel, ' - - - ')
collabels = [' File /Group Name ', 'External Value', 'Predicted Value']
colsizes = [300, 120, 120]
coltypes = ['str', 'float:12,4', 'float:12,4']
coldefs = ['', 0.0, 0.0]
wids['table'] = DataTableGrid(panel,
nrows=MAX_ROWS,
collabels=collabels,
datatypes=coltypes,
defaults=coldefs,
colsizes=colsizes)
wids['table'].SetMinSize((625, 175))
wids['use_selected'] = Button(panel,
'Use Selected Groups',
size=(150, -1),
action=self.onFillTable)
panel.Add(SimpleText(panel, 'Feature Regression, Model Selection',
**self.titleopts),
dcol=4)
add_text('Array to Use: ', newrow=True)
panel.Add(wids['fitspace'], dcol=4)
# add_text('Plot : ', newrow=True)
# panel.Add(wids['plotchoice'], dcol=3)
add_text('Fit Energy Range: ')
panel.Add(w_xmin)
add_text(' : ', newrow=False)
panel.Add(w_xmax, dcol=3)
add_text('Regression Method:')
panel.Add(wids['method'], dcol=4)
add_text('PLS # components: ')
panel.Add(w_ncomps)
panel.Add(wids['auto_scale_pls'], dcol=2)
add_text('Lasso Alpha: ')
panel.Add(wids['alpha'])
panel.Add(wids['auto_alpha'], dcol=2)
panel.Add(wids['fit_intercept'])
wids['alpha'].Disable()
wids['auto_alpha'].Disable()
wids['fit_intercept'].Disable()
add_text('Cross Validation: ')
add_text(' # folds, # repeats: ', newrow=False)
panel.Add(w_cvfolds, dcol=2)
panel.Add(w_cvreps)
panel.Add(HLine(panel, size=(600, 2)), dcol=6, newrow=True)
add_text('Build Model: ', newrow=True)
panel.Add(wids['use_selected'], dcol=2)
add_text('Attribute Name: ', newrow=False)
panel.Add(wids['varname'], dcol=4)
add_text('Read/Save Data: ', newrow=True)
panel.Add(wids['load_csv'], dcol=3)
panel.Add(wids['save_csv'], dcol=2)
panel.Add(wids['table'], newrow=True, dcol=5) # , drow=3)
panel.Add(HLine(panel, size=(550, 2)), dcol=5, newrow=True)
panel.Add((5, 5), newrow=True)
add_text('Train Model : ')
panel.Add(wids['train_model'], dcol=3)
panel.Add(wids['load_model'])
add_text('Use This Model : ')
panel.Add(wids['fit_group'], dcol=3)
panel.Add(wids['save_model'])
add_text('Fit Statistics : ')
panel.Add(wids['stat1'], dcol=4)
panel.Add((5, 5), newrow=True)
panel.Add(wids['stat2'], dcol=4)
panel.pack()
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add((10, 10), 0, LEFT, 3)
sizer.Add(panel, 1, LEFT, 3)
pack(self, sizer)
self.skip_process = False
def build_display(self):
panel = self.panel
wids = self.wids
self.skip_process = True
wids['fitspace'] = Choice(panel,
choices=FitSpace_Choices,
size=(175, -1))
wids['fitspace'].SetStringSelection(norm)
add_text = self.add_text
opts = dict(digits=2, increment=1.0, relative_e0=False) # True)
elo_wids = self.add_floatspin('elo', value=defaults['elo'], **opts)
ehi_wids = self.add_floatspin('ehi', value=defaults['ehi'], **opts)
wids['fit_group'] = Button(panel,
'Fit this Group',
size=(175, -1),
action=self.onFitOne)
wids['fit_selected'] = Button(panel,
'Fit Selected Groups',
size=(175, -1),
action=self.onFitAll)
wids['add_selected'] = Button(panel,
'Use Selected Groups as Components',
size=(300, -1),
action=self.onUseSelected)
wids['saveconf'] = Button(panel,
'Save as Default Settings',
size=(225, -1),
action=self.onSaveConfigBtn)
opts = dict(default=True, size=(75, -1), action=self.onPlotOne)
wids['show_fitrange'] = Check(panel, label='show?', **opts)
wids['sum_to_one'] = Check(panel,
label='Weights Must Sum to 1?',
default=True)
wids['all_combos'] = Check(panel,
label='Fit All Combinations?',
default=True)
max_ncomps = self.add_floatspin('max_ncomps',
value=10,
digits=0,
increment=1,
min_val=0,
max_val=20,
size=(60, -1),
with_pin=False)
panel.Add(SimpleText(panel, ' Linear Combination Analysis',
**self.titleopts),
dcol=4)
add_text('Array to Fit: ', newrow=True)
panel.Add(wids['fitspace'], dcol=3)
add_text('Fit Energy Range: ')
panel.Add(elo_wids)
add_text(' : ', newrow=False)
panel.Add(ehi_wids)
panel.Add(wids['show_fitrange'])
panel.Add(HLine(panel, size=(625, 3)), dcol=5, newrow=True)
add_text('Run Fit: ')
panel.Add(wids['fit_group'], dcol=2)
panel.Add(wids['fit_selected'], dcol=3)
add_text('Fit Options: ')
panel.Add(wids['sum_to_one'], dcol=2)
panel.Add((10, 10), dcol=1, newrow=True)
panel.Add(wids['all_combos'], dcol=2)
add_text('Max # Components: ', newrow=False)
panel.Add(max_ncomps, dcol=2)
panel.Add(HLine(panel, size=(625, 3)), dcol=5, newrow=True)
add_text('Components: ')
panel.Add(wids['add_selected'], dcol=4)
collabels = [' File /Group Name ', 'weight', 'min', 'max']
colsizes = [300, 80, 80, 80]
coltypes = ['str', 'float:12,4', 'float:12,4', 'float:12,4']
coldefs = ['', 1.0 / MAX_COMPONENTS, 0.0, 1.0]
wids['table'] = DataTableGrid(panel,
nrows=MAX_COMPONENTS,
collabels=collabels,
datatypes=coltypes,
defaults=coldefs,
colsizes=colsizes)
wids['table'].SetMinSize((625, 250))
panel.Add(wids['table'], newrow=True, dcol=6)
panel.Add(HLine(panel, size=(625, 3)), dcol=5, newrow=True)
panel.Add(wids['saveconf'], dcol=4, newrow=True)
panel.pack()
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add((10, 10), 0, LEFT, 3)
sizer.Add(panel, 1, LEFT, 3)
pack(self, sizer)
self.skip_process = False
def build(self):
sizer = wx.GridBagSizer(5, 5)
sizer.SetVGap(5)
sizer.SetHGap(5)
splitter = wx.SplitterWindow(self, style=wx.SP_LIVE_UPDATE)
splitter.SetMinimumPaneSize(200)
self.datalistbox = EditableListBox(splitter,
self.ShowDataSet,
size=(250, -1))
panel = scrolled.ScrolledPanel(splitter)
self.SetMinSize((650, 600))
self.colors = GUIColors()
# title row
self.wids = wids = {}
title = SimpleText(panel,
'Linear Combination Results',
font=Font(FONTSIZE + 2),
colour=self.colors.title,
style=LEFT)
wids['plot_one'] = Button(panel,
'Plot This Fit',
size=(125, -1),
action=self.onPlotOne)
wids['plot_sel'] = Button(panel,
'Plot N Best Fits',
size=(125, -1),
action=self.onPlotSel)
wids['plot_ntitle'] = SimpleText(panel, 'N fits to plot: ')
wids['plot_nchoice'] = Choice(panel,
size=(60, -1),
choices=['%d' % i for i in range(1, 21)])
wids['plot_nchoice'].SetStringSelection('5')
wids['data_title'] = SimpleText(panel,
'<--> ',
font=Font(FONTSIZE + 2),
colour=self.colors.title,
style=LEFT)
wids['nfits_title'] = SimpleText(panel, 'showing 5 best fits')
copts = dict(size=(125, 30), default=True, action=self.onPlotOne)
# wids['show_e0'] = Check(panel, label='show E0?', **copts)
wids['show_fitrange'] = Check(panel, label='show fit range?', **copts)
irow = 0
sizer.Add(title, (irow, 0), (1, 1), LEFT)
sizer.Add(wids['data_title'], (irow, 1), (1, 2), LEFT)
irow += 1
sizer.Add(wids['nfits_title'], (irow, 0), (1, 1), LEFT)
irow += 1
self.wids['paramstitle'] = SimpleText(panel,
'[[Parameters]]',
font=Font(FONTSIZE + 2),
colour=self.colors.title,
style=LEFT)
sizer.Add(self.wids['paramstitle'], (irow, 0), (1, 1), LEFT)
pview = self.wids['params'] = dv.DataViewListCtrl(panel, style=DVSTYLE)
pview.SetMinSize((475, 200))
pview.AppendTextColumn(' Parameter ', width=230)
pview.AppendTextColumn(' Best-Fit Value', width=120)
pview.AppendTextColumn(' Standard Error ', width=120)
for col in range(3):
this = pview.Columns[col]
isort, align = True, wx.ALIGN_RIGHT
if col == 0:
align = wx.ALIGN_LEFT
this.Sortable = isort
this.Alignment = this.Renderer.Alignment = align
irow += 1
sizer.Add(self.wids['params'], (irow, 0), (4, 1), LEFT)
sizer.Add(self.wids['plot_one'], (irow, 1), (1, 2), LEFT)
sizer.Add(self.wids['plot_sel'], (irow + 1, 1), (1, 2), LEFT)
sizer.Add(self.wids['plot_ntitle'], (irow + 2, 1), (1, 1), LEFT)
sizer.Add(self.wids['plot_nchoice'], (irow + 2, 2), (1, 1), LEFT)
# sizer.Add(self.wids['show_e0'], (irow+3, 1), (1, 2), LEFT)
sizer.Add(self.wids['show_fitrange'], (irow + 3, 1), (1, 2), LEFT)
irow += 4
sizer.Add(HLine(panel, size=(675, 3)), (irow, 0), (1, 4), LEFT)
sview = self.wids['stats'] = dv.DataViewListCtrl(panel, style=DVSTYLE)
sview.Bind(dv.EVT_DATAVIEW_SELECTION_CHANGED, self.onSelectFitStat)
sview.AppendTextColumn(' Fit #', width=50)
sview.AppendTextColumn(' N_vary', width=50)
sview.AppendTextColumn(' N_eval', width=60)
sview.AppendTextColumn(' \u03c7\u00B2', width=110)
sview.AppendTextColumn(' \u03c7\u00B2_reduced', width=110)
sview.AppendTextColumn(' Akaike Info', width=110)
sview.AppendTextColumn(' Bayesian Info', width=110)
for col in range(sview.ColumnCount):
this = sview.Columns[col]
isort, align = True, wx.ALIGN_RIGHT
if col == 0:
align = wx.ALIGN_CENTER
this.Sortable = isort
this.Alignment = this.Renderer.Alignment = align
sview.SetMinSize((675, 175))
irow += 1
title = SimpleText(panel,
'[[Fit Statistics]]',
font=Font(FONTSIZE + 2),
colour=self.colors.title,
style=LEFT)
sizer.Add(title, (irow, 0), (1, 4), LEFT)
irow += 1
sizer.Add(sview, (irow, 0), (1, 4), LEFT)
irow += 1
sizer.Add(HLine(panel, size=(675, 3)), (irow, 0), (1, 4), LEFT)
irow += 1
title = SimpleText(panel,
'[[Weights]]',
font=Font(FONTSIZE + 2),
colour=self.colors.title,
style=LEFT)
sizer.Add(title, (irow, 0), (1, 4), LEFT)
self.wids['weightspanel'] = ppan = wx.Panel(panel)
p1 = SimpleText(ppan, ' < Weights > ')
os = wx.BoxSizer(wx.VERTICAL)
os.Add(p1, 1, 3)
pack(ppan, os)
ppan.SetMinSize((675, 175))
irow += 1
sizer.Add(ppan, (irow, 0), (1, 4), LEFT)
irow += 1
sizer.Add(HLine(panel, size=(675, 3)), (irow, 0), (1, 4), LEFT)
pack(panel, sizer)
panel.SetupScrolling()
splitter.SplitVertically(self.datalistbox, panel, 1)
mainsizer = wx.BoxSizer(wx.VERTICAL)
mainsizer.Add(splitter, 1, wx.GROW | wx.ALL, 5)
pack(self, mainsizer)
# self.SetSize((725, 750))
self.Show()
self.Raise()
def build_display(self):
titleopts = dict(font=Font(12), colour='#AA0000')
panel = self.panel
wids = self.wids
self.skip_process = True
wids['fitspace'] = Choice(panel,
choices=FitSpace_Choices,
size=(175, -1))
wids['fitspace'].SetStringSelection(norm)
wids['plotchoice'] = Choice(panel,
choices=Plot_Choices,
size=(175, -1),
action=self.onPlot)
wids['plotchoice'].SetSelection(1)
add_text = self.add_text
opts = dict(digits=2, increment=1.0, relative_e0=True)
e0_wids = self.add_floatspin('e0', value=0, **opts)
elo_wids = self.add_floatspin('elo', value=-20, **opts)
ehi_wids = self.add_floatspin('ehi', value=30, **opts)
wids['fit_group'] = Button(panel,
'Fit this Group',
size=(150, -1),
action=self.onFitOne)
wids['fit_selected'] = Button(panel,
'Fit Selected Groups',
size=(150, -1),
action=self.onFitAll)
wids['add_selected'] = Button(panel,
'Use Selected Groups as Components',
size=(250, -1),
action=self.onUseSelected)
wids['saveconf'] = Button(panel,
'Save as Default Settings',
size=(200, -1),
action=self.onSaveConfigBtn)
opts = dict(default=True, size=(75, -1), action=self.onPlotOne)
wids['show_e0'] = Check(panel, label='show?', **opts)
wids['show_fitrange'] = Check(panel, label='show?', **opts)
wids['sum_to_one'] = Check(panel,
label='Weights Must Sum to 1?',
default=True)
wids['all_combos'] = Check(panel,
label='Fit All Combinations?',
default=True)
panel.Add(SimpleText(panel, ' Linear Combination Analysis',
**titleopts),
dcol=5)
add_text('Run Fit', newrow=False)
add_text('Array to Fit: ', newrow=True)
panel.Add(wids['fitspace'], dcol=4)
panel.Add(wids['fit_group'])
add_text('Plot : ', newrow=True)
panel.Add(wids['plotchoice'], dcol=4)
panel.Add(wids['fit_selected'])
add_text('E0: ')
panel.Add(e0_wids, dcol=3)
panel.Add(wids['show_e0'])
add_text('Fit Energy Range: ')
panel.Add(elo_wids)
add_text(' : ', newrow=False)
panel.Add(ehi_wids)
panel.Add(wids['show_fitrange'])
panel.Add(wids['sum_to_one'], dcol=2, newrow=True)
panel.Add(wids['all_combos'], dcol=3)
panel.Add(HLine(panel, size=(400, 2)), dcol=5, newrow=True)
add_text('Components: ')
panel.Add(wids['add_selected'], dcol=4)
groupnames = [noname] + list(self.controller.file_groups.keys())
sgrid = GridPanel(panel, nrows=6)
sgrid.Add(SimpleText(sgrid, "#"))
sgrid.Add(SimpleText(sgrid, "Group"))
sgrid.Add(SimpleText(sgrid, "Weight"))
sgrid.Add(SimpleText(sgrid, "Min Weight"))
sgrid.Add(SimpleText(sgrid, "Max Weight"))
fopts = dict(minval=-10, maxval=20, precision=4, size=(60, -1))
for i in range(1, 1 + MAX_COMPONENTS):
si = ("comp", "_%2.2d" % i)
sgrid.Add(SimpleText(sgrid, "%2i" % i), newrow=True)
wids['%schoice%s' % si] = Choice(sgrid,
choices=groupnames,
size=(200, -1),
action=partial(self.onComponent,
comp=i))
wids['%sval%s' % si] = FloatCtrl(sgrid, value=0, **fopts)
wids['%smin%s' % si] = FloatCtrl(sgrid, value=0, **fopts)
wids['%smax%s' % si] = FloatCtrl(sgrid, value=1, **fopts)
for cname in ('choice', 'val', 'min', 'max'):
sgrid.Add(wids[("%%s%s%%s" % cname) % si])
sgrid.pack()
panel.Add(sgrid, dcol=5, newrow=True)
panel.Add(HLine(panel, size=(400, 2)), dcol=5, newrow=True)
panel.Add(wids['saveconf'], dcol=4, newrow=True)
panel.pack()
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add(panel, 1, LCEN, 3)
pack(self, sizer)
self.skip_process = False
def build(self):
sizer = wx.GridBagSizer(10, 5)
sizer.SetVGap(5)
sizer.SetHGap(5)
panel = scrolled.ScrolledPanel(self)
self.SetMinSize((675, 600))
self.colors = GUIColors()
# title row
self.wids = wids = {}
title = SimpleText(panel,
'Linear Combination Results',
font=Font(12),
colour=self.colors.title,
style=LCEN)
wids['plot_one'] = Button(panel,
'Plot This Fit',
size=(150, -1),
action=self.onPlotOne)
wids['plot_sel'] = Button(panel,
'Plot top N Fits',
size=(150, -1),
action=self.onPlotSel)
wids['plot_ntitle'] = SimpleText(panel, 'N fits to plot: ')
wids['plot_nchoice'] = Choice(panel,
size=(100, -1),
choices=['%d' % i for i in range(1, 21)])
wids['plot_nchoice'].SetStringSelection('5')
wids['data_title'] = SimpleText(panel,
'<--> ',
font=Font(12),
colour=self.colors.title,
style=LCEN)
wids['nfits_title'] = SimpleText(panel, 'showing top 5 fits')
irow = 0
sizer.Add(title, (irow, 0), (1, 2), LCEN)
sizer.Add(wids['data_title'], (irow, 2), (1, 2), LCEN)
irow += 1
sizer.Add(wids['nfits_title'], (irow, 0), (1, 4), LCEN)
irow += 1
sizer.Add(self.wids['plot_one'], (irow, 0), (1, 1), LCEN)
sizer.Add(self.wids['plot_sel'], (irow, 1), (1, 1), LCEN)
sizer.Add(self.wids['plot_ntitle'], (irow, 2), (1, 1), LCEN)
sizer.Add(self.wids['plot_nchoice'], (irow, 3), (1, 1), LCEN)
irow += 1
self.wids['paramstitle'] = SimpleText(panel,
'[[Parameters]]',
font=Font(12),
colour=self.colors.title,
style=LCEN)
sizer.Add(self.wids['paramstitle'], (irow, 0), (1, 4), LCEN)
pview = self.wids['params'] = dv.DataViewListCtrl(panel, style=DVSTYLE)
pview.SetMinSize((675, 200))
pview.AppendTextColumn(' Parameter ', width=250)
pview.AppendTextColumn(' Best-Fit Value', width=150)
pview.AppendTextColumn(' Uncertainty ', width=150)
for col in range(3):
this = pview.Columns[col]
isort, align = True, wx.ALIGN_RIGHT
if col == 0:
align = wx.ALIGN_LEFT
this.Sortable = isort
this.Alignment = this.Renderer.Alignment = align
irow += 1
sizer.Add(self.wids['params'], (irow, 0), (1, 4), LCEN)
irow += 1
sizer.Add(HLine(panel, size=(675, 3)), (irow, 0), (1, 4), LCEN)
sview = self.wids['stats'] = dv.DataViewListCtrl(panel, style=DVSTYLE)
sview.Bind(dv.EVT_DATAVIEW_SELECTION_CHANGED, self.onSelectFitStat)
sview.AppendTextColumn(' Fit #', width=50)
sview.AppendTextColumn(' N_Vary', width=60)
sview.AppendTextColumn(' N_Data', width=60)
sview.AppendTextColumn(' N_eval', width=60)
sview.AppendTextColumn(u' \u03c7\u00B2', width=100)
sview.AppendTextColumn(u' \u03c7\u00B2_reduced', width=100)
sview.AppendTextColumn(' Akaike Info', width=100)
sview.AppendTextColumn(' Bayesian Info', width=100)
for col in range(8):
this = sview.Columns[col]
isort, align = True, wx.ALIGN_RIGHT
if col == 0:
align = wx.ALIGN_CENTER
this.Sortable = isort
this.Alignment = this.Renderer.Alignment = align
sview.SetMinSize((675, 175))
irow += 1
title = SimpleText(panel,
'[[Fit Statistics]]',
font=Font(12),
colour=self.colors.title,
style=LCEN)
sizer.Add(title, (irow, 0), (1, 4), LCEN)
irow += 1
sizer.Add(sview, (irow, 0), (1, 4), LCEN)
irow += 1
sizer.Add(HLine(panel, size=(675, 3)), (irow, 0), (1, 4), LCEN)
irow += 1
title = SimpleText(panel,
'[[Weights]]',
font=Font(12),
colour=self.colors.title,
style=LCEN)
sizer.Add(title, (irow, 0), (1, 4), LCEN)
self.wids['weightspanel'] = ppan = wx.Panel(self)
p1 = SimpleText(ppan, ' < Weights > ')
os = wx.BoxSizer(wx.VERTICAL)
os.Add(p1, 1, 3)
pack(ppan, os)
ppan.SetMinSize((675, 175))
irow += 1
sizer.Add(ppan, (irow, 0), (1, 4), LCEN)
irow += 1
sizer.Add(HLine(panel, size=(675, 3)), (irow, 0), (1, 4), LCEN)
pack(panel, sizer)
panel.SetupScrolling()
mainsizer = wx.BoxSizer(wx.VERTICAL)
mainsizer.Add(panel, 1, wx.GROW | wx.ALL, 1)
pack(self, mainsizer)
self.Show()
self.Raise()
def build_display(self):
self.mod_nb = flatnotebook(self, {})
pan = self.panel = GridPanel(self, ncols=4, nrows=4, pad=2, itemstyle=LEFT)
self.wids = {}
fsopts = dict(digits=2, increment=0.1, with_pin=True)
ppeak_e0 = self.add_floatspin('ppeak_e0', value=0, **fsopts)
ppeak_elo = self.add_floatspin('ppeak_elo', value=-15, **fsopts)
ppeak_ehi = self.add_floatspin('ppeak_ehi', value=-5, **fsopts)
ppeak_emin = self.add_floatspin('ppeak_emin', value=-30, **fsopts)
ppeak_emax = self.add_floatspin('ppeak_emax', value=0, **fsopts)
self.fitbline_btn = Button(pan,'Fit Baseline', action=self.onFitBaseline,
size=(125, -1))
self.plotmodel_btn = Button(pan, 'Plot Model',
action=self.onPlotModel, size=(125, -1))
self.fitmodel_btn = Button(pan, 'Fit Model',
action=self.onFitModel, size=(125, -1))
self.loadmodel_btn = Button(pan, 'Load Model',
action=self.onLoadFitResult, size=(125, -1))
self.fitmodel_btn.Disable()
self.array_choice = Choice(pan, size=(175, -1),
choices=list(Array_Choices.keys()))
self.array_choice.SetSelection(1)
models_peaks = Choice(pan, size=(150, -1),
choices=ModelChoices['peaks'],
action=self.addModel)
models_other = Choice(pan, size=(150, -1),
choices=ModelChoices['other'],
action=self.addModel)
self.models_peaks = models_peaks
self.models_other = models_other
self.message = SimpleText(pan,
'first fit baseline, then add peaks to fit model.')
self.msg_centroid = SimpleText(pan, '----')
opts = dict(default=True, size=(75, -1), action=self.onPlot)
self.show_centroid = Check(pan, label='show?', **opts)
self.show_peakrange = Check(pan, label='show?', **opts)
self.show_fitrange = Check(pan, label='show?', **opts)
self.show_e0 = Check(pan, label='show?', **opts)
opts = dict(default=False, size=(200, -1), action=self.onPlot)
def add_text(text, dcol=1, newrow=True):
pan.Add(SimpleText(pan, text), dcol=dcol, newrow=newrow)
pan.Add(SimpleText(pan, ' Pre-edge Peak Fitting',
**self.titleopts), dcol=5)
add_text(' Run Fit:', newrow=False)
add_text('Array to fit: ')
pan.Add(self.array_choice, dcol=3)
pan.Add((10, 10))
pan.Add(self.fitbline_btn)
add_text('E0: ')
pan.Add(ppeak_e0)
pan.Add((10, 10), dcol=2)
pan.Add(self.show_e0)
pan.Add(self.plotmodel_btn)
add_text('Fit Energy Range: ')
pan.Add(ppeak_emin)
add_text(' : ', newrow=False)
pan.Add(ppeak_emax)
pan.Add(self.show_fitrange)
pan.Add(self.fitmodel_btn)
t = SimpleText(pan, 'Pre-edge Peak Range: ')
SetTip(t, 'Range used as mask for background')
pan.Add(t, newrow=True)
pan.Add(ppeak_elo)
add_text(' : ', newrow=False)
pan.Add(ppeak_ehi)
pan.Add(self.show_peakrange)
# pan.Add(self.fitsel_btn)
add_text( 'Peak Centroid: ')
pan.Add(self.msg_centroid, dcol=3)
pan.Add(self.show_centroid, dcol=1)
pan.Add(self.loadmodel_btn)
# add model
ts = wx.BoxSizer(wx.HORIZONTAL)
ts.Add(models_peaks)
ts.Add(models_other)
pan.Add(SimpleText(pan, 'Add Component: '), newrow=True)
pan.Add(ts, dcol=7)
pan.Add(SimpleText(pan, 'Messages: '), newrow=True)
pan.Add(self.message, dcol=7)
pan.pack()
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add((10, 10), 0, LEFT, 3)
sizer.Add(pan, 0, LEFT, 3)
sizer.Add((10, 10), 0, LEFT, 3)
sizer.Add(HLine(self, size=(550, 2)), 0, LEFT, 3)
sizer.Add((10, 10), 0, LEFT, 3)
sizer.Add(self.mod_nb, 1, LEFT|wx.GROW, 10)
pack(self, sizer)
def addModel(self, event=None, model=None, prefix=None, isbkg=False):
if model is None and event is not None:
model = event.GetString()
if model is None or model.startswith('<'):
return
if prefix is None:
p = model[:5].lower()
curmodels = ["%s%i_" % (p, 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)
title = prefix[:-1]
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:
if model in ModelFuncs:
mclass = getattr(lm_models, ModelFuncs[model])
else:
mclass = getattr(lm_models, model+'Model')
minst = mclass(prefix=prefix)
panel = GridPanel(self.mod_nb, ncols=2, nrows=5, pad=2, 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 in Fit?', size=(100, -1))
bkgbox = Check(panel, default=False, label='Is Baseline?', size=(125, -1))
if isbkg:
bkgbox.SetValue(1)
delbtn = Button(panel, 'Delete Component', size=(125, -1),
action=partial(self.onDeleteComponent, prefix=prefix))
pick2msg = SimpleText(panel, " ", size=(125, -1))
pick2btn = Button(panel, 'Pick Values from Data', size=(150, -1),
action=partial(self.onPick2Points, prefix=prefix))
# SetTip(mname, 'Label for the model component')
SetTip(usebox, 'Use this component in fit?')
SetTip(bkgbox, 'Label this component as "background" when plotting?')
SetTip(delbtn, 'Delete this model component')
SetTip(pick2btn, 'Select X range on Plot to Guess Initial Values')
panel.Add(SLabel(label, size=(275, -1), colour='#0000AA'),
dcol=3, style=wx.ALIGN_LEFT, newrow=True)
panel.Add(usebox, dcol=1)
panel.Add(bkgbox, dcol=2, style=LCEN)
panel.Add(delbtn, dcol=1, style=wx.ALIGN_LEFT)
panel.Add(pick2btn, dcol=2, style=wx.ALIGN_LEFT, newrow=True)
panel.Add(pick2msg, dcol=2, style=wx.ALIGN_RIGHT)
# panel.Add((10, 10), newrow=True)
# panel.Add(HLine(panel, size=(150, 3)), dcol=4, style=wx.ALIGN_CENTER)
panel.Add(SLabel("Parameter "), style=wx.ALIGN_LEFT, newrow=True)
panel.AddMany((SLabel(" Value"), SLabel(" Type"), SLabel(' Bounds'),
SLabel(" Min", size=(60, -1)),
SLabel(" Max", size=(60, -1)), 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=100, expr_size=125,
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.bounds,
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=100, expr_size=225,
float_size=80, prefix=prefix,
widgets=('name', 'value', 'expr'))
parwids[par.name] = pwids
panel.Add(pwids.name, newrow=True)
panel.Add(pwids.value)
panel.Add(pwids.expr, dcol=4, style=wx.ALIGN_RIGHT)
pwids.value.Disable()
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, bkgbox=bkgbox)
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 SLabel(label, size=(80, -1), **kws):
return SimpleText(panel, label,
size=size, style=wx.ALIGN_LEFT, **kws)
def build_display(self):
panel = self.panel
wids = self.wids
self.skip_process = True
wids['fitspace'] = Choice(panel,
choices=FitSpace_Choices,
size=(175, -1))
wids['fitspace'].SetStringSelection(norm)
wids['plotchoice'] = Choice(panel,
choices=Plot_Choices,
size=(175, -1),
action=self.onPlot)
wids['plotchoice'].SetSelection(0)
add_text = self.add_text
opts = dict(digits=2, increment=1.0)
w_xmin = self.add_floatspin('xmin', value=defaults['xmin'], **opts)
w_xmax = self.add_floatspin('xmax', value=defaults['xmax'], **opts)
w_wmin = self.add_floatspin('weight_min',
digits=4,
value=defaults['weight_min'],
increment=0.001,
with_pin=False,
min_val=0,
max_val=0.5,
action=self.onSet_WeightMin)
autoset_fs_increment(self.wids['weight_min'], defaults['weight_min'])
self.wids['weight_auto'] = Check(panel, default=True, label='auto?')
w_mcomps = self.add_floatspin('max_components',
digits=0,
value=defaults['max_components'],
increment=1,
with_pin=False,
min_val=0)
b_build_model = Button(panel,
'Build Model With Selected Groups',
size=(275, -1),
action=self.onBuildPCAModel)
wids['fit_group'] = Button(panel,
'Test Current Group with Model',
size=(225, -1),
action=self.onFitGroup)
wids['save_model'] = Button(panel,
'Save PCA Model',
size=(150, -1),
action=self.onSavePCAModel)
wids['load_model'] = Button(panel,
'Load PCA Model',
size=(150, -1),
action=self.onLoadPCAModel)
wids['fit_group'].Disable()
wids['load_model'].Disable()
wids['save_model'].Disable()
collabels = [
' Variance ', ' IND value ', ' IND / IND_Best', ' Factor Weight'
]
colsizes = [100, 100, 100, 200]
coltypes = ['float:12,6', 'float:12,6', 'float:12,5', 'string']
coldefs = [0.0, 0.0, 1.0, '0.0']
wids['table'] = DataTableGrid(panel,
nrows=MAX_ROWS,
collabels=collabels,
datatypes=coltypes,
defaults=coldefs,
colsizes=colsizes,
rowlabelsize=60)
wids['table'].SetMinSize((625, 175))
wids['table'].EnableEditing(False)
#
# sview = self.wids['stats'] = dv.DataViewListCtrl(panel, style=DVSTYLE)
# sview.AppendTextColumn(' Component', width=75)
# sview.AppendTextColumn(' Weight', width=100)
# sview.AppendTextColumn(' Significant?', width=75)
#
# for col in range(sview.ColumnCount):
# this = sview.Columns[col]
# align = wx.ALIGN_LEFT if col == 0 else wx.ALIGN_RIGHT
# this.Sortable = False
# this.Alignment = this.Renderer.Alignment = align
# sview.SetMinSize((275, 250))
wids['status'] = SimpleText(panel, ' ')
rfont = self.GetFont()
rfont.SetPointSize(rfont.GetPointSize() + 1)
wids['fit_chi2'] = SimpleText(panel, '0.000', font=rfont)
wids['fit_dscale'] = SimpleText(panel, '1.000', font=rfont)
panel.Add(SimpleText(panel, ' Principal Component Analysis',
**self.titleopts),
dcol=4)
add_text('Array to Use: ', newrow=True)
panel.Add(wids['fitspace'], dcol=2)
panel.Add(wids['load_model'], dcol=2)
add_text('Plot : ', newrow=True)
panel.Add(wids['plotchoice'], dcol=2)
panel.Add(wids['save_model'], dcol=2)
add_text('Fit Energy Range: ')
panel.Add(w_xmin)
add_text(' : ', newrow=False)
panel.Add(w_xmax)
#panel.Add(wids['show_fitrange'])
add_text('Min Weight: ')
panel.Add(w_wmin)
panel.Add(wids['weight_auto'])
add_text('Max Components:', dcol=1, newrow=True)
panel.Add(w_mcomps)
panel.Add(Button(panel,
'Copy To Selected Groups',
size=(200, -1),
action=partial(self.onCopyParam, 'pca')),
dcol=2)
add_text('Status: ')
panel.Add(wids['status'], dcol=3)
panel.Add(HLine(panel, size=(550, 2)), dcol=5, newrow=True)
panel.Add(b_build_model, dcol=5, newrow=True)
panel.Add(wids['table'], dcol=5, newrow=True)
panel.Add(wids['fit_group'], dcol=3, newrow=True)
add_text('chi-square: ')
panel.Add(wids['fit_chi2'])
add_text('scale factor: ')
panel.Add(wids['fit_dscale'])
#
# ## add weights report: slightly tricky layout
# ## working with GridBagSizer under gridpanel...
# icol = panel.icol - 2
# irow = panel.irow
# pstyle, ppad = panel.itemstyle, panel.pad
#
# panel.sizer.Add(SimpleText(panel, 'data scalefactor = '),
# (irow+1, icol), (1, 1), pstyle, ppad)
# panel.sizer.Add(wids['fit_dscale'],
# (irow+1, icol+1), (1, 1), pstyle, ppad)
# irow +=1
# for i in range(1, NWTS+1):
# wids['fit_wt%d' % i] = SimpleText(panel, '--', font=rfont)
# panel.sizer.Add(SimpleText(panel, 'weight_%d ='%i, font=rfont),
# (irow+i, icol), (1, 1), pstyle, ppad)
# panel.sizer.Add(wids['fit_wt%d'%i],
# (irow+i, icol+1), (1, 1), pstyle, ppad)
#
panel.pack()
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add((10, 10), 0, LCEN, 3)
sizer.Add(panel, 1, LCEN, 3)
pack(self, sizer)
self.skip_process = False
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 build_display(self):
titleopts = dict(font=Font(12), colour='#AA0000')
panel = self.panel
wids = self.wids
self.skip_process = True
wids['plotone_op'] = Choice(panel,
choices=PlotOne_Choices,
action=self.onPlotOne,
size=(175, -1))
wids['plotalt_op'] = Choice(panel,
choices=PlotAlt_Choices,
action=self.onPlotOne,
size=(175, -1))
wids['plotsel_op'] = Choice(panel,
choices=PlotSel_Choices,
action=self.onPlotSel,
size=(175, -1))
wids['plotone_op'].SetStringSelection(chik)
wids['plotsel_op'].SetStringSelection(chik)
wids['plotalt_op'].SetStringSelection(noplot)
plot_one = Button(panel,
'Plot This Group',
size=(150, -1),
action=self.onPlotOne)
plot_sel = Button(panel,
'Plot Selected Groups',
size=(150, -1),
action=self.onPlotSel)
saveconf = Button(panel,
'Save as Default Settings',
size=(200, -1),
action=self.onSaveConfigBtn)
def FloatSpinWithPin(name, value, **kws):
s = wx.BoxSizer(wx.HORIZONTAL)
self.wids[name] = FloatSpin(panel, value=value, **kws)
bb = BitmapButton(panel,
get_icon('pin'),
size=(25, 25),
action=partial(self.onSelPoint, opt=name),
tooltip='use last point selected from plot')
s.Add(wids[name])
s.Add(bb)
return s
wids['plot_voffset'] = FloatSpin(panel,
value=0,
digits=2,
increment=0.25,
action=self.onProcess)
wids['plot_kweight'] = FloatSpin(panel,
value=2,
digits=1,
increment=1,
action=self.onProcess,
min_val=0,
max_val=5)
wids['plot_kweight_alt'] = FloatSpin(panel,
value=2,
digits=1,
increment=1,
action=self.onProcess,
min_val=0,
max_val=5)
opts = dict(digits=2, increment=0.1, min_val=0, action=self.onProcess)
wids['e0'] = FloatSpin(panel, **opts)
opts['max_val'] = 5
wids['rbkg'] = FloatSpin(panel, value=1.0, **opts)
opts['max_val'] = 125
bkg_kmin = FloatSpinWithPin('bkg_kmin', value=0, **opts)
bkg_kmax = FloatSpinWithPin('bkg_kmax', value=20, **opts)
fft_kmin = FloatSpinWithPin('fft_kmin', value=0, **opts)
fft_kmax = FloatSpinWithPin('fft_kmax', value=20, **opts)
wids['fft_dk'] = FloatSpin(panel, value=3, **opts)
opts.update({'increment': 1, 'digits': 1, 'max_val': 5})
wids['bkg_kweight'] = FloatSpin(panel, value=1, **opts)
wids['fft_kweight'] = FloatSpin(panel, value=1, **opts)
opts = dict(choices=CLAMPLIST, size=(80, -1), action=self.onProcess)
wids['bkg_clamplo'] = Choice(panel, **opts)
wids['bkg_clamphi'] = Choice(panel, **opts)
wids['fft_kwindow'] = Choice(panel,
choices=list(FTWINDOWS),
action=self.onProcess,
size=(125, -1))
def add_text(text, dcol=1, newrow=True):
panel.Add(SimpleText(panel, text), dcol=dcol, newrow=newrow)
panel.Add(SimpleText(panel, ' EXAFS Processing', **titleopts), dcol=5)
panel.Add(plot_sel, newrow=True)
panel.Add(self.wids['plotsel_op'], dcol=2)
add_text('Vertical offset: ', newrow=False)
panel.Add(wids['plot_voffset'], dcol=2)
panel.Add(plot_one, newrow=True)
panel.Add(self.wids['plotone_op'], dcol=2)
add_text('Plot k weight: ', newrow=False)
panel.Add(wids['plot_kweight'])
add_text('Add Second Plot: ', newrow=True)
panel.Add(self.wids['plotalt_op'], dcol=2)
add_text('Plot2 k weight: ', newrow=False)
panel.Add(wids['plot_kweight_alt'])
panel.Add(HLine(panel, size=(500, 3)), dcol=6, newrow=True)
panel.Add(SimpleText(panel, ' Background subtraction', **titleopts),
dcol=2,
newrow=True)
panel.Add(Button(panel,
'Copy To Selected Groups',
size=(175, -1),
action=partial(self.onCopyParam, 'bkg')),
dcol=2)
add_text('R bkg: ')
panel.Add(wids['rbkg'])
add_text('E0: ', newrow=False)
panel.Add(wids['e0'])
add_text('k min: ')
panel.Add(bkg_kmin)
add_text('k max:', newrow=False)
panel.Add(bkg_kmax)
add_text('kweight: ', newrow=True)
panel.Add(wids['bkg_kweight'], dcol=1)
add_text('Clamps Low E: ', newrow=True)
panel.Add(wids['bkg_clamplo'])
add_text('high E: ', newrow=False)
panel.Add(wids['bkg_clamphi'])
panel.Add(HLine(panel, size=(500, 3)), dcol=6, newrow=True)
panel.Add(SimpleText(panel, ' Fourier transform', **titleopts),
dcol=2,
newrow=True)
panel.Add(Button(panel,
'Copy to Selected Groups',
size=(175, -1),
action=partial(self.onCopyParam, 'fft')),
dcol=2)
panel.Add(SimpleText(panel, 'k min: '), newrow=True)
panel.Add(fft_kmin)
panel.Add(SimpleText(panel, 'k max:'))
panel.Add(fft_kmax)
panel.Add(SimpleText(panel, 'k weight : '), newrow=True)
panel.Add(wids['fft_kweight'])
panel.Add(SimpleText(panel, 'K window : '), newrow=True)
panel.Add(wids['fft_kwindow'])
panel.Add(SimpleText(panel, ' dk : '))
panel.Add(wids['fft_dk'])
panel.Add(HLine(panel, size=(500, 3)), dcol=6, newrow=True)
panel.Add(saveconf, dcol=4, newrow=True)
panel.pack()
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add(panel, 1, LCEN, 3)
pack(self, sizer)
self.skip_process = False
def add_text(self, text, dcol=1, newrow=True):
self.panel.Add(SimpleText(self.panel, text), dcol=dcol, newrow=newrow)
def build(self):
sizer = wx.GridBagSizer(10, 5)
sizer.SetVGap(5)
sizer.SetHGap(5)
panel = scrolled.ScrolledPanel(self)
self.SetMinSize((600, 450))
self.colors = GUIColors()
# title row
self.wids = wids = {}
title = SimpleText(panel, 'Fit Results', font=Font(12),
colour=self.colors.title, style=LCEN)
wids['data_title'] = SimpleText(panel, '< > ', font=Font(12),
colour=self.colors.title, style=LCEN)
wids['hist_info'] = SimpleText(panel, ' ___ ', font=Font(12),
colour=self.colors.title, style=LCEN)
sizer.Add(title, (0, 0), (1, 2), LCEN)
sizer.Add(wids['data_title'], (0, 2), (1, 2), LCEN)
sizer.Add(wids['hist_info'], (0, 4), (1, 2), LCEN)
irow = 1
wids['model_desc'] = SimpleText(panel, '<Model>', font=Font(12),
size=(550, 75), style=LCEN)
sizer.Add(wids['model_desc'], (irow, 0), (1, 6), LCEN)
irow += 1
sizer.Add(HLine(panel, size=(400, 3)), (irow, 0), (1, 5), LCEN)
irow += 1
title = SimpleText(panel, '[[Fit Statistics]]', font=Font(12),
colour=self.colors.title, style=LCEN)
sizer.Add(title, (irow, 0), (1, 4), LCEN)
for label, attr in (('Fit method', 'method'),
('# Fit Evaluations', 'nfev'),
('# Data Points', 'ndata'),
('# Fit Variables', 'nvarys'),
('# Free Points', 'nfree'),
('Chi-square', 'chisqr'),
('Reduced Chi-square', 'redchi'),
('Akaike Info Criteria', 'aic'),
('Bayesian Info Criteria', 'bic')):
irow += 1
wids[attr] = SimpleText(panel, '?')
sizer.Add(SimpleText(panel, " %s = " % label), (irow, 0), (1, 1), LCEN)
sizer.Add(wids[attr], (irow, 1), (1, 1), LCEN)
irow += 1
sizer.Add(HLine(panel, size=(400, 3)), (irow, 0), (1, 5), LCEN)
irow += 1
title = SimpleText(panel, '[[Variables]]', font=Font(12),
colour=self.colors.title, style=LCEN)
sizer.Add(title, (irow, 0), (1, 1), LCEN)
self.wids['copy_params'] = Button(panel, 'Update Model with Best Fit Values',
size=(250, -1), action=self.onCopyParams)
sizer.Add(self.wids['copy_params'], (irow, 1), (1, 3), LCEN)
dvstyle = dv.DV_SINGLE|dv.DV_VERT_RULES|dv.DV_ROW_LINES
pview = self.wids['params'] = dv.DataViewListCtrl(panel, style=dvstyle)
self.wids['paramsdata'] = []
pview.AppendTextColumn('Parameter', width=150)
pview.AppendTextColumn('Best-Fit Value', width=100)
pview.AppendTextColumn('Standard Error', width=100)
pview.AppendTextColumn('Info ', width=275)
for col in (0, 1, 2, 3):
this = pview.Columns[col]
isort, align = True, wx.ALIGN_LEFT
if col in (1, 2):
isort, align = False, wx.ALIGN_RIGHT
this.Sortable = isort
this.Alignment = this.Renderer.Alignment = align
pview.SetMinSize((650, 200))
pview.Bind(dv.EVT_DATAVIEW_SELECTION_CHANGED, self.onSelectParameter)
irow += 1
sizer.Add(pview, (irow, 0), (1, 5), LCEN)
irow += 1
sizer.Add(HLine(panel, size=(400, 3)), (irow, 0), (1, 5), LCEN)
irow += 1
title = SimpleText(panel, '[[Correlations]]', font=Font(12),
colour=self.colors.title, style=LCEN)
self.wids['all_correl'] = Button(panel, 'Show All',
size=(100, -1), action=self.onAllCorrel)
self.wids['min_correl'] = FloatSpin(panel, value=MIN_CORREL,
min_val=0, size=(60, -1),
digits=3, increment=0.1)
ctitle = SimpleText(panel, 'minimum correlation: ')
sizer.Add(title, (irow, 0), (1, 1), LCEN)
sizer.Add(ctitle, (irow, 1), (1, 1), LCEN)
sizer.Add(self.wids['min_correl'], (irow, 2), (1, 1), LCEN)
sizer.Add(self.wids['all_correl'], (irow, 3), (1, 1), LCEN)
irow += 1
cview = self.wids['correl'] = dv.DataViewListCtrl(panel, style=dvstyle)
cview.AppendTextColumn('Parameter 1', width=150)
cview.AppendTextColumn('Parameter 2', width=150)
cview.AppendTextColumn('Correlation', width=100)
for col in (0, 1, 2):
this = cview.Columns[col]
isort, align = True, wx.ALIGN_LEFT
if col == 1:
isort = False
if col == 2:
align = wx.ALIGN_RIGHT
this.Sortable = isort
this.Alignment = this.Renderer.Alignment = align
cview.SetMinSize((450, 200))
irow += 1
sizer.Add(cview, (irow, 0), (1, 5), LCEN)
irow += 1
sizer.Add(HLine(panel, size=(400, 3)), (irow, 0), (1, 5), LCEN)
pack(panel, sizer)
panel.SetupScrolling()
mainsizer = wx.BoxSizer(wx.VERTICAL)
mainsizer.Add(panel, 1, wx.GROW|wx.ALL, 1)
pack(self, mainsizer)
self.Show()
self.Raise()
def createMainPanel(self):
display0 = wx.Display(0)
client_area = display0.ClientArea
xmin, ymin, xmax, ymax = client_area
xpos = int((xmax - xmin) * 0.02) + xmin
ypos = int((ymax - ymin) * 0.04) + ymin
self.SetPosition((xpos, ypos))
splitter = wx.SplitterWindow(self, style=wx.SP_LIVE_UPDATE)
splitter.SetMinimumPaneSize(250)
leftpanel = wx.Panel(splitter)
ltop = wx.Panel(leftpanel)
def Btn(msg, x, act):
b = Button(ltop, msg, size=(x, 30), action=act)
b.SetFont(Font(FONTSIZE))
return b
sel_none = Btn('Select None', 120, self.onSelNone)
sel_all = Btn('Select All', 120, self.onSelAll)
self.controller.filelist = FileCheckList(
leftpanel,
# main=self,
select_action=self.ShowFile,
remove_action=self.RemoveFile)
tsizer = wx.BoxSizer(wx.HORIZONTAL)
tsizer.Add(sel_all, 1, LCEN | wx.GROW, 1)
tsizer.Add(sel_none, 1, LCEN | wx.GROW, 1)
pack(ltop, tsizer)
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add(ltop, 0, LCEN | wx.GROW, 1)
sizer.Add(self.controller.filelist, 1, LCEN | wx.GROW | wx.ALL, 1)
pack(leftpanel, sizer)
# right hand side
panel = wx.Panel(splitter)
sizer = wx.BoxSizer(wx.VERTICAL)
self.title = SimpleText(panel, 'initializing...', size=(300, -1))
self.title.SetFont(Font(FONTSIZE + 1))
ir = 0
sizer.Add(self.title, 0, LCEN | wx.GROW | wx.ALL, 1)
self.nb = flat_nb.FlatNotebook(panel, -1, agwStyle=FNB_STYLE)
self.nb.SetTabAreaColour(wx.Colour(250, 250, 250))
self.nb.SetActiveTabColour(wx.Colour(254, 254, 195))
self.nb.SetNonActiveTabTextColour(wx.Colour(10, 10, 128))
self.nb.SetActiveTabTextColour(wx.Colour(128, 0, 0))
self.nb_panels = []
for name, creator in NB_PANELS:
_panel = creator(parent=self, controller=self.controller)
self.nb.AddPage(_panel, " %s " % name, True)
self.nb_panels.append(_panel)
sizer.Add(self.nb, 1, LCEN | wx.EXPAND, 2)
self.nb.Bind(wx.EVT_NOTEBOOK_PAGE_CHANGED, self.onNBChanged)
self.nb.SetSelection(0)
pack(panel, sizer)
splitter.SplitVertically(leftpanel, panel, 1)
wx.CallAfter(self.init_larch)
def build(self):
sizer = wx.GridBagSizer(10, 5)
sizer.SetVGap(5)
sizer.SetHGap(5)
panel = scrolled.ScrolledPanel(self)
self.SetMinSize((700, 450))
self.colors = GUIColors()
# title row
self.wids = wids = {}
title = SimpleText(panel, 'Fit Results', font=Font(FONTSIZE+2),
colour=self.colors.title, style=LEFT)
wids['data_title'] = SimpleText(panel, '< > ', font=Font(FONTSIZE+2),
colour=self.colors.title, style=LEFT)
wids['hist_info'] = SimpleText(panel, ' ___ ', font=Font(FONTSIZE+2),
colour=self.colors.title, style=LEFT)
wids['hist_hint'] = SimpleText(panel, ' (Fit #01 is most recent)',
font=Font(FONTSIZE+2), colour=self.colors.title,
style=LEFT)
opts = dict(default=False, size=(200, -1), action=self.onPlot)
wids['plot_bline'] = Check(panel, label='Plot baseline-subtracted?', **opts)
wids['plot_resid'] = Check(panel, label='Plot with residual?', **opts)
self.plot_choice = Button(panel, 'Plot Selected Fit',
size=(175, -1), action=self.onPlot)
self.save_result = Button(panel, 'Save Selected Model',
size=(175, -1), action=self.onSaveFitResult)
SetTip(self.save_result, 'save model and result to be loaded later')
self.export_fit = Button(panel, 'Export Fit',
size=(175, -1), action=self.onExportFitResult)
SetTip(self.export_fit, 'save arrays and results to text file')
irow = 0
sizer.Add(title, (irow, 0), (1, 2), LEFT)
sizer.Add(wids['data_title'], (irow, 2), (1, 2), LEFT)
irow += 1
sizer.Add(wids['hist_info'], (irow, 0), (1, 2), LEFT)
sizer.Add(wids['hist_hint'], (irow, 2), (1, 2), LEFT)
irow += 1
wids['model_desc'] = SimpleText(panel, '<Model>', font=Font(FONTSIZE+1),
size=(700, 50), style=LEFT)
sizer.Add(wids['model_desc'], (irow, 0), (1, 6), LEFT)
irow += 1
sizer.Add(self.save_result, (irow, 0), (1, 1), LEFT)
sizer.Add(self.export_fit, (irow, 1), (1, 2), LEFT)
irow += 1
# sizer.Add(SimpleText(panel, 'Plot: '), (irow, 0), (1, 1), LEFT)
sizer.Add(self.plot_choice, (irow, 0), (1, 2), LEFT)
sizer.Add(wids['plot_bline'], (irow, 2), (1, 1), LEFT)
sizer.Add(wids['plot_resid'], (irow, 3), (1, 1), LEFT)
irow += 1
sizer.Add(HLine(panel, size=(650, 3)), (irow, 0), (1, 5), LEFT)
irow += 1
title = SimpleText(panel, '[[Fit Statistics]]', font=Font(FONTSIZE+2),
colour=self.colors.title, style=LEFT)
sizer.Add(title, (irow, 0), (1, 4), LEFT)
sview = self.wids['stats'] = dv.DataViewListCtrl(panel, style=DVSTYLE)
sview.Bind(dv.EVT_DATAVIEW_SELECTION_CHANGED, self.onSelectFit)
sview.AppendTextColumn(' Fit #', width=50)
sview.AppendTextColumn(' N_data', width=50)
sview.AppendTextColumn(' N_vary', width=50)
sview.AppendTextColumn(' N_eval', width=60)
sview.AppendTextColumn(' \u03c7\u00B2', width=110)
sview.AppendTextColumn(' \u03c7\u00B2_reduced', width=110)
sview.AppendTextColumn(' Akaike Info', width=110)
sview.AppendTextColumn(' Bayesian Info', width=110)
for col in range(sview.ColumnCount):
this = sview.Columns[col]
isort, align = True, wx.ALIGN_RIGHT
if col == 0:
align = wx.ALIGN_CENTER
this.Sortable = isort
this.Alignment = this.Renderer.Alignment = align
sview.SetMinSize((700, 125))
irow += 1
sizer.Add(sview, (irow, 0), (1, 5), LEFT)
irow += 1
sizer.Add(HLine(panel, size=(650, 3)), (irow, 0), (1, 5), LEFT)
irow += 1
title = SimpleText(panel, '[[Variables]]', font=Font(FONTSIZE+2),
colour=self.colors.title, style=LEFT)
sizer.Add(title, (irow, 0), (1, 1), LEFT)
self.wids['copy_params'] = Button(panel, 'Update Model with these values',
size=(250, -1), action=self.onCopyParams)
sizer.Add(self.wids['copy_params'], (irow, 1), (1, 3), LEFT)
pview = self.wids['params'] = dv.DataViewListCtrl(panel, style=DVSTYLE)
self.wids['paramsdata'] = []
pview.AppendTextColumn('Parameter', width=150)
pview.AppendTextColumn('Best-Fit Value', width=125)
pview.AppendTextColumn('Standard Error', width=125)
pview.AppendTextColumn('Info ', width=275)
for col in range(4):
this = pview.Columns[col]
align = wx.ALIGN_LEFT
if col in (1, 2):
align = wx.ALIGN_RIGHT
this.Sortable = False
this.Alignment = this.Renderer.Alignment = align
pview.SetMinSize((700, 200))
pview.Bind(dv.EVT_DATAVIEW_SELECTION_CHANGED, self.onSelectParameter)
irow += 1
sizer.Add(pview, (irow, 0), (1, 5), LEFT)
irow += 1
sizer.Add(HLine(panel, size=(650, 3)), (irow, 0), (1, 5), LEFT)
irow += 1
title = SimpleText(panel, '[[Correlations]]', font=Font(FONTSIZE+2),
colour=self.colors.title, style=LEFT)
self.wids['all_correl'] = Button(panel, 'Show All',
size=(100, -1), action=self.onAllCorrel)
self.wids['min_correl'] = FloatSpin(panel, value=MIN_CORREL,
min_val=0, size=(100, -1),
digits=3, increment=0.1)
ctitle = SimpleText(panel, 'minimum correlation: ')
sizer.Add(title, (irow, 0), (1, 1), LEFT)
sizer.Add(ctitle, (irow, 1), (1, 1), LEFT)
sizer.Add(self.wids['min_correl'], (irow, 2), (1, 1), LEFT)
sizer.Add(self.wids['all_correl'], (irow, 3), (1, 1), LEFT)
irow += 1
cview = self.wids['correl'] = dv.DataViewListCtrl(panel, style=DVSTYLE)
cview.AppendTextColumn('Parameter 1', width=150)
cview.AppendTextColumn('Parameter 2', width=150)
cview.AppendTextColumn('Correlation', width=150)
for col in (0, 1, 2):
this = cview.Columns[col]
this.Sortable = False
align = wx.ALIGN_LEFT
if col == 2:
align = wx.ALIGN_RIGHT
this.Alignment = this.Renderer.Alignment = align
cview.SetMinSize((475, 200))
irow += 1
sizer.Add(cview, (irow, 0), (1, 5), LEFT)
irow += 1
sizer.Add(HLine(panel, size=(400, 3)), (irow, 0), (1, 5), LEFT)
pack(panel, sizer)
panel.SetupScrolling()
mainsizer = wx.BoxSizer(wx.VERTICAL)
mainsizer.Add(panel, 1, wx.GROW|wx.ALL, 1)
pack(self, mainsizer)
self.Show()
self.Raise()