class PlotterFrame(wx.Frame):
_about = """StepScan 2D Plotter
Matt Newville <newville @ cars.uchicago.edu>
"""
def __init__(self, dbname=None, server='sqlite', host=None,
port=None, user=None, password=None, create=True, **kws):
wx.Frame.__init__(self, None, -1, style=FRAMESTYLE)
self.data = None
self.filemap = {}
title = "Step Scan Data File Viewer"
self.scandb = None
if dbname is not None:
self.scandb = ScanDB(dbname=dbname, server=server, host=host,
user=user, password=password, port=port,
create=create)
self.filemap[CURSCAN] = SCANGROUP
title = '%s, with Live Scan Viewing' % title
self.larch = None
self.plotters = []
self.SetTitle(title)
self.SetSize((850, 650))
self.SetFont(Font(9))
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)
if dbname is not None:
self.live_scanfile = None
self.live_cpt = -1
self.filelist.Append(CURSCAN)
self.scantimer = wx.Timer(self)
self.Bind(wx.EVT_TIMER, self.onScanTimer, self.scantimer)
self.scantimer.Start(250)
def onScanTimer(self, evt=None, **kws):
if self.larch is None:
return
group = getattr(self.larch.symtable, SCANGROUP)
curfile = fix_filename(self.scandb.get_info('filename'))
if curfile != self.live_scanfile:
self.live_scanfile = curfile
group.filename = self.live_scanfile
group.array_units = []
self.live_cpt = -1
sdata = self.scandb.get_scandata()
if len(sdata) <= 1:
return
npts = len(sdata[-1].data)
if npts <= self.live_cpt:
return
self.live_cpt = npts
if len(group.array_units) < 1:
group.array_units = [str(row.notes) for row in sdata]
for row in sdata:
setattr(group, fix_filename(row.name), np.array(row.data))
if npts > 1:
self.onPlot()
def createMainPanel(self):
splitter = wx.SplitterWindow(self, style=wx.SP_LIVE_UPDATE)
splitter.SetMinimumPaneSize(175)
self.filelist = wx.ListBox(splitter)
self.filelist.SetBackgroundColour(wx.Colour(255, 255, 255))
self.filelist.Bind(wx.EVT_LISTBOX, self.ShowFile)
self.detailspanel = self.createDetailsPanel(splitter)
splitter.SplitVertically(self.filelist, self.detailspanel, 1)
wx.CallAfter(self.init_larch)
def createDetailsPanel(self, parent):
mainpanel = wx.Panel(parent)
mainsizer = wx.BoxSizer(wx.VERTICAL)
panel = wx.Panel(mainpanel)
sizer = wx.GridBagSizer(8, 7)
self.title = SimpleText(panel, 'initializing...')
ir = 0
sizer.Add(self.title, (ir, 0), (1, 6), LCEN, 2)
# x-axis
self.xarr = add_choice(panel, choices=[],
action=self.onYchoice, size=(120, -1))
self.xop = add_choice(panel, choices=('', 'log'),
action=self.onYchoice, size=(75, -1))
ir += 1
sizer.Add(SimpleText(panel, 'X = '), (ir, 0), (1, 1), CEN, 0)
sizer.Add(self.xop, (ir, 1), (1, 1), CEN, 0)
sizer.Add(SimpleText(panel, '('), (ir, 2), (1, 1), CEN, 0)
sizer.Add(self.xarr, (ir, 3), (1, 1), RCEN, 0)
sizer.Add(SimpleText(panel, ')'), (ir, 4), (1, 1), CEN, 0)
self.yops = [[],[]]
self.yarr = [[],[]]
for opts, sel, siz in ((PRE_OPS, 0, 75), (ARR_OPS, 3, 50),
(ARR_OPS, 3, 50)):
w1 = add_choice(panel, choices=opts, action=self.onYchoice,
size=(siz, -1))
w1.SetSelection(sel)
self.yops[0].append(w1)
w2 = add_choice(panel, choices=opts, action=self.onYchoice,
size=(siz, -1))
w2.SetSelection(sel)
self.yops[1].append(w2)
opts= {'choices':[], 'size':(120, -1), 'action':self.onYchoice}
for i in range(3):
self.yarr[0].append(add_choice(panel, **opts))
self.yarr[1].append(add_choice(panel, **opts))
for i in range(2):
ir += 1
label = 'Y%i = ' % (i+1)
sizer.Add(SimpleText(panel, label), (ir, 0), (1, 1), CEN, 0)
sizer.Add(self.yops[i][0], (ir, 1), (1, 1), CEN, 0)
sizer.Add(SimpleText(panel, '[('), (ir, 2), (1, 1), CEN, 0)
sizer.Add(self.yarr[i][0], (ir, 3), (1, 1), CEN, 0)
sizer.Add(self.yops[i][1], (ir, 4), (1, 1), CEN, 0)
sizer.Add(self.yarr[i][1], (ir, 5), (1, 1), CEN, 0)
sizer.Add(SimpleText(panel, ')'), (ir, 6), (1, 1), LCEN, 0)
sizer.Add(self.yops[i][2], (ir, 7), (1, 1), CEN, 0)
sizer.Add(self.yarr[i][2], (ir, 8), (1, 1), CEN, 0)
sizer.Add(SimpleText(panel, ']'), (ir, 9), (1, 1), LCEN, 0)
ir += 1
# sizer.Add(SimpleText(panel, ' New Plot: '), (ir, 0), (1, 3), LCEN, 0)
# sizer.Add(SimpleText(panel, ' Over Plot: '), (ir+1, 0), (1, 3), LCEN, 0)
for jr, ic, dc, opt, ttl in ((0, 0, 4, 'win old', 'New Plot, This Window'),
(0, 4, 2, 'win new', 'New Plot, New Window'),
(1, 0, 4, 'over left', 'Over Plot, Left Axis'),
(1, 4, 2, 'over right', 'Over Plot, Right Axis')):
sizer.Add(add_button(panel, ttl, size=(165, -1),
action=Closure(self.onPlot, opt=opt)),
(ir+jr, ic), (1, dc), LCEN, 2)
ir += 2
self.dtcorr = check(panel, default=True, label='correct deadtime?')
sizer.Add(self.dtcorr, (ir, 0), (1, 3), LCEN, 0)
ir += 1
sizer.Add(SimpleText(panel, ''), (ir, 0), (1, 3), LCEN, 0)
pack(panel, sizer)
# self.nb = flat_nb.FlatNotebook(mainpanel, -1, agwStyle=FNB_STYLE)
#
# self.nb.SetTabAreaColour(wx.Colour(248,248,240))
# self.nb.SetActiveTabColour(wx.Colour(254,254,195))
#
# self.nb.SetNonActiveTabTextColour(wx.Colour(40,40,180))
# self.nb.SetActiveTabTextColour(wx.Colour(80,0,0))
#
# self.xas_panel = self.CreateXASPanel(self.nb) # mainpanel)
# self.fit_panel = self.CreateFitPanel(self.nb) # mainpanel)
#
# self.nb.AddPage(self.fit_panel, ' General Analysis ', True)
# self.nb.AddPage(self.xas_panel, ' XAS Processing ', True)
mainsizer.Add(panel, 0, LCEN|wx.EXPAND, 2)
self.plotpanel = PlotPanel(mainpanel, size=(500, 670))
self.plotpanel.messenger = self.write_message
bgcol = panel.GetBackgroundColour()
bgcol = (bgcol[0]/255., bgcol[1]/255., bgcol[2]/255.)
self.plotpanel.canvas.figure.set_facecolor(bgcol)
mainsizer.Add(self.plotpanel, 1, wx.GROW|wx.ALL, 1)
# mainsizer.Add(self.nb, 1, LCEN|wx.EXPAND, 2)
pack(mainpanel, mainsizer)
return mainpanel
def CreateFitPanel(self, parent):
p = panel = wx.Panel(parent)
self.fit_model = add_choice(panel, size=(100, -1),
choices=('Gaussian', 'Lorentzian',
'Voigt', 'Linear', 'Quadratic',
'Step', 'Rectangle',
'Exponential'))
self.fit_bkg = add_choice(panel, size=(100, -1),
choices=('None', 'constant', 'linear', 'quadtratic'))
self.fit_step = add_choice(panel, size=(100, -1),
choices=('linear', 'error function', 'arctan'))
self.fit_report = wx.StaticText(panel, -1, "", (180, 200))
sizer = wx.GridBagSizer(10, 4)
sizer.Add(SimpleText(p, 'Fit Model: '), (0, 0), (1, 1), LCEN)
sizer.Add(self.fit_model, (0, 1), (1, 1), LCEN)
sizer.Add(SimpleText(p, 'Background: '), (1, 0), (1, 1), LCEN)
sizer.Add(self.fit_bkg, (1, 1), (1, 1), LCEN)
sizer.Add(SimpleText(p, 'Step Function Form: '), (2, 0), (1, 1), LCEN)
sizer.Add(self.fit_step, (2, 1), (1, 1), LCEN)
sizer.Add(add_button(panel, 'Show Fit', size=(100, -1),
action=self.onFitPeak), (3, 0), (1, 1), LCEN)
sizer.Add(self.fit_report, (0, 2), (4, 2), LCEN, 3)
pack(panel, sizer)
return panel
def CreateXASPanel(self, parent):
p = panel = wx.Panel(parent)
self.xas_autoe0 = check(panel, default=True, label='auto?')
self.xas_autostep = check(panel, default=True, label='auto?')
self.xas_op = add_choice(panel, size=(95, -1),
choices=('Raw Data', 'Pre-edged',
'Normalized', 'Flattened'))
self.xas_e0 = FloatCtrl(panel, value = 0, precision=3, size=(95, -1))
self.xas_step = FloatCtrl(panel, value = 0, precision=3, size=(95, -1))
self.xas_pre1 = FloatCtrl(panel, value=-200, precision=1, size=(95, -1))
self.xas_pre2 = FloatCtrl(panel, value= -30, precision=1, size=(95, -1))
self.xas_nor1 = FloatCtrl(panel, value= 30, precision=1, size=(95, -1))
self.xas_nor2 = FloatCtrl(panel, value= 300, precision=1, size=(95, -1))
self.xas_vict = add_choice(panel, size=(50, -1), choices=('0', '1', '2', '3'))
self.xas_nnor = add_choice(panel, size=(50, -1), choices=('0', '1', '2', '3'))
self.xas_vict.SetSelection(1)
self.xas_nnor.SetSelection(2)
sizer = wx.GridBagSizer(10, 4)
sizer.Add(SimpleText(p, 'Plot XAS as: '), (0, 0), (1, 1), LCEN)
sizer.Add(SimpleText(p, 'E0 : '), (1, 0), (1, 1), LCEN)
sizer.Add(SimpleText(p, 'Edge Step: '), (2, 0), (1, 1), LCEN)
sizer.Add(SimpleText(p, 'Pre-edge range: '), (3, 0), (1, 1), LCEN)
sizer.Add(SimpleText(p, 'Normalization range: '), (4, 0), (1, 1), LCEN)
sizer.Add(self.xas_op, (0, 1), (1, 1), LCEN)
sizer.Add(self.xas_e0, (1, 1), (1, 1), LCEN)
sizer.Add(self.xas_step, (2, 1), (1, 1), LCEN)
sizer.Add(self.xas_pre1, (3, 1), (1, 1), LCEN)
sizer.Add(SimpleText(p, ':'), (3, 2), (1, 1), LCEN)
sizer.Add(self.xas_pre2, (3, 3), (1, 1), LCEN)
sizer.Add(self.xas_nor1, (4, 1), (1, 1), LCEN)
sizer.Add(SimpleText(p, ':'), (4, 2), (1, 1), LCEN)
sizer.Add(self.xas_nor2, (4, 3), (1, 1), LCEN)
sizer.Add(self.xas_autoe0, (1, 2), (1, 2), LCEN)
sizer.Add(self.xas_autostep, (2, 2), (1, 2), LCEN)
sizer.Add(SimpleText(p, 'Victoreen:'), (3, 4), (1, 1), LCEN)
sizer.Add(self.xas_vict, (3, 5), (1, 1), LCEN)
sizer.Add(SimpleText(p, 'PolyOrder:'), (4, 4), (1, 1), LCEN)
sizer.Add(self.xas_nnor, (4, 5), (1, 1), LCEN)
pack(panel, sizer)
return panel
def onFitPeak(self, evt=None):
gname = self.groupname
if self.dtcorr.IsChecked():
print('fit needs to dt correct!')
dtext = []
model = self.fit_model.GetStringSelection().lower()
dtext.append('Fit Model: %s' % model)
bkg = self.fit_bkg.GetStringSelection()
if bkg == 'None':
bkg = None
if bkg is None:
dtext.append('No Background')
else:
dtext.append('Background: %s' % bkg)
step = self.fit_step.GetStringSelection().lower()
if model in ('step', 'rectangle'):
dtext.append('Step form: %s' % step)
lgroup = getattr(self.larch.symtable, gname)
x = lgroup._x1_
y = lgroup._y1_
pgroup = fit_peak(x, y, model, background=bkg, step=step,
_larch=self.larch)
text = fit_report(pgroup.params, _larch=self.larch)
dtext.append('Parameters: ')
for pname in dir(pgroup.params):
par = getattr(pgroup.params, pname)
if isParameter(par):
ptxt = " %s= %.4f" % (par.name, par.value)
if (hasattr(par, 'stderr') and par.stderr is not None):
ptxt = "%s(%.4f)" % (ptxt, par.stderr)
dtext.append(ptxt)
dtext = '\n'.join(dtext)
# plotframe = self.get_plotwindow()
# plotframe.oplot(x, pgroup.fit, label='fit (%s)' % model)
text = fit_report(pgroup.params, _larch=self.larch)
self.fit_report.SetLabel(dtext)
def xas_process(self, gname, plotopts):
""" process (pre-edge/normalize) XAS data from XAS form, overwriting
larch group '_y1_' attribute to be plotted
"""
out = self.xas_op.GetStringSelection().lower() # raw, pre, norm, flat
if out.startswith('raw'):
return plotopts
preopts = {'group': gname, 'e0': None, 'step': None}
lgroup = getattr(self.larch.symtable, gname)
if self.dtcorr.IsChecked():
print( 'need to dt correct!')
if not self.xas_autoe0.IsChecked():
xmin, xmax = min(lgroup._x1_), max(lgroup._x1_)
e0 = self.xas_e0.GetValue()
if e0 < xmax and e0 > xmin:
preopts['e0'] = e0
if not self.xas_autostep.IsChecked():
preopts['step'] = self.xas_step.GetValue()
preopts['pre1'] = self.xas_pre1.GetValue()
preopts['pre2'] = self.xas_pre2.GetValue()
preopts['norm1'] = self.xas_nor1.GetValue()
preopts['norm2'] = self.xas_nor2.GetValue()
preopts['nvict'] = self.xas_vict.GetSelection()
preopts['nnorm'] = self.xas_nnor.GetSelection()
preopts = ", ".join(["%s=%s" %(k, v) for k,v in preopts.items()])
preedge_cmd = "pre_edge(%s._x1_, %s._y1_, %s)" % (gname, gname, preopts)
self.larch(preedge_cmd)
self.xas_e0.SetValue(lgroup.e0)
self.xas_step.SetValue(lgroup.edge_step)
if out.startswith('pre'):
self.larch('%s._y1_ = %s.norm * %s.edge_step' % (gname, gname, gname))
elif out.startswith('norm'):
self.larch('%s._y1_ = %s.norm' % (gname, gname))
elif out.startswith('flat'):
self.larch('%s._y1_ = %s.flat' % (gname, gname))
return plotopts
def init_larch(self):
t0 = time.time()
from larch.wxlib import inputhook
self.larch = Interpreter()
self.larch.symtable.set_symbol('_sys.wx.wxapp', wx.GetApp())
self.larch.symtable.set_symbol('_sys.wx.parent', self)
self.larch('%s = group(filename="%s")' % (SCANGROUP, CURSCAN))
self.SetStatusText('ready')
self.datagroups = self.larch.symtable
self.title.SetLabel('')
def write_message(self, s, panel=0):
"""write a message to the Status Bar"""
self.SetStatusText(s, panel)
def get_plotwindow(self, new=False, **kws):
pframe = None
if not new:
while pframe is None:
try:
pframe = self.plotters.pop()
pframe.Show()
pframe.Raise()
except IndexError:
pframe = None
break
except PyDeadObjectError:
pframe = None
if pframe is None:
pframe = PlotFrame()
pframe.Show()
pframe.Raise()
self.plotters.append(pframe)
return pframe
def onYchoice(self, evt=None, side='left'):
self.onPlot()
def onPlot(self, evt=None, opt='new old', npts=None):
# 'win new', 'New Window'),
# 'win old', 'Old Window'),
# 'over left', 'Left Axis'),
# 'over right', 'Right Axis')):
# 'update left', from scan
optwords = opt.split()
# plotframe = self.get_plotwindow(new=('new' in optwords[1]))
# plotcmd = plotframe.plot
plotcmd = self.plotpanel.plot
optwords = opt.split()
side = 'left'
update = False
if optwords[0] == 'over':
side = optwords[1]
plotcmd = self.plotpanel.oplot
elif optwords[0] == 'update' and npts > 4:
plotcmd = self.plotpanel.update_line
update = True
popts = {'side': side}
ix = self.xarr.GetSelection()
x = self.xarr.GetStringSelection()
try:
gname = self.groupname
lgroup = getattr(self.larch.symtable, gname)
except:
gname = SCANGROUP
lgroup = getattr(self.larch.symtable, gname)
xfmt = "%s._x1_ = %s(%s)"
yfmt = "%s._y1_ = %s((%s %s %s) %s (%s))"
xop = self.xop.GetStringSelection()
xlabel = x
try:
xunits = lgroup.array_units[ix]
except:
xunits = ''
if xop != '':
xlabel = "%s(%s)" % (xop, xlabel)
if xunits != '':
xlabel = '%s (%s)' % (xlabel, xunits)
popts['xlabel'] = xlabel
opl1 = self.yops[0][0].GetStringSelection()
opl2 = self.yops[0][1].GetStringSelection()
opl3 = self.yops[0][2].GetStringSelection()
yl1 = self.yarr[0][0].GetStringSelection()
yl2 = self.yarr[0][1].GetStringSelection()
yl3 = self.yarr[0][2].GetStringSelection()
opr1 = self.yops[1][0].GetStringSelection()
opr2 = self.yops[1][1].GetStringSelection()
opr3 = self.yops[1][2].GetStringSelection()
yr1 = self.yarr[1][0].GetStringSelection()
yr2 = self.yarr[1][1].GetStringSelection()
yr3 = self.yarr[1][2].GetStringSelection()
ylabel = yl1
if yl2 == '':
yl2, opl2 = '1', '*'
else:
ylabel = "%s%s%s" % (ylabel, opl2, yl2)
if yl3 == '':
yl3, opl3 = '1', '*'
else:
ylabel = "(%s)%s%s" % (ylabel, opl3, yl3)
if opl1 != '':
ylabel = "%s(%s)" % (opl1, ylabel)
if yl1 not in ('0', '1'): yl1 = "%s.%s" % (gname, yl1)
if yl2 not in ('0', '1'): yl2 = "%s.%s" % (gname, yl2)
if yl3 not in ('0', '1'): yl3 = "%s.%s" % (gname, yl3)
if x not in ('0', '1'): x = "%s.%s" % (gname, x)
self.larch(xfmt % (gname, xop, x))
self.larch(yfmt % (gname, opl1, yl1, opl2, yl2, opl3, yl3))
try:
npts = min(len(lgroup._x1_), len(lgroup._y1_))
except AttributeError:
return
lgroup._x1_ = np.array( lgroup._x1_[:npts])
lgroup._y1_ = np.array( lgroup._y1_[:npts])
path, fname = os.path.split(lgroup.filename)
popts['label'] = "%s: %s" % (fname, ylabel)
if side == 'right':
popts['y2label'] = ylabel
else:
popts['ylabel'] = ylabel
if plotcmd == self.plotpanel.plot:
popts['title'] = fname
# XAFS Processing!
#if (self.nb.GetCurrentPage() == self.xas_panel):
# popts = self.xas_process(gname, popts)
if update:
self.plotpanel.set_xlabel(popts['xlabel'])
self.plotpanel.set_ylabel(popts['ylabel'])
plotcmd(0, lgroup._x1_, lgroup._y1_, draw=True,
update_limits=True) # ((npts < 5) or (npts % 5 == 0)))
self.plotpanel.set_xylims((
min(lgroup._x1_), max(lgroup._x1_),
min(lgroup._y1_), max(lgroup._y1_)))
else:
plotcmd(lgroup._x1_, lgroup._y1_, **popts)
self.plotpanel.canvas.draw()
def ShowFile(self, evt=None, filename=None, **kws):
if filename is None and evt is not None:
filename = evt.GetString()
key = filename
if filename in self.filemap:
key = self.filemap[filename]
if key == SCANGROUP:
array_labels = [fix_filename(s.name) for s in self.scandb.get_scandata()]
title = filename
elif hasattr(self.datagroups, key):
data = getattr(self.datagroups, key)
title = data.filename
array_labels = data.array_labels[:]
self.groupname = key
xcols = array_labels[:]
ycols = array_labels[:]
y2cols = array_labels[:] + ['1.0', '0.0', '']
ncols = len(xcols)
self.title.SetLabel(title)
self.xarr.SetItems(xcols)
self.xarr.SetSelection(0)
self.xop.SetSelection(0)
for i in range(2):
for j in range(3):
self.yarr[i][j].SetItems(y2cols)
self.yarr[i][j].SetSelection(len(y2cols))
if i == 0:
self.yarr[i][0].SetItems(ycols)
self.yarr[i][0].SetSelection(1)
inb = 0
for colname in xcols:
if 'energ' in colname.lower():
inb = 1
#self.nb.SetSelection(inb)
def createMenus(self):
# ppnl = self.plotpanel
self.menubar = wx.MenuBar()
#
fmenu = wx.Menu()
pmenu = wx.Menu()
add_menu(self, fmenu, "&Open Scan File\tCtrl+O",
"Read Scan File", self.onReadScan)
fmenu.AppendSeparator()
add_menu(self, fmenu, "&Quit\tCtrl+Q", "Quit program", self.onClose)
self.menubar.Append(fmenu, "&File")
# fmenu.AppendSeparator()
# add_menu(self, fmenu, "&Copy\tCtrl+C",
# "Copy Figure to Clipboard", self.onClipboard)
# add_menu(self, fmenu, "&Save\tCtrl+S", "Save Figure", self.onSaveFig)
# add_menu(self, fmenu, "&Print\tCtrl+P", "Print Figure", self.onPrint)
# add_menu(self, fmenu, "Page Setup", "Print Page Setup", self.onPrintSetup)
# add_menu(self, fmenu, "Preview", "Print Preview", self.onPrintPreview)
#
# add_menu(self, pmenu, "Configure\tCtrl+K",
# "Configure Plot", self.onConfigurePlot)
#add_menu(self, pmenu, "Unzoom\tCtrl+Z", "Unzoom Plot", self.onUnzoom)
##pmenu.AppendSeparator()
#add_menu(self, pmenu, "Toggle Legend\tCtrl+L",
# "Toggle Legend on Plot", self.onToggleLegend)
#add_menu(self, pmenu, "Toggle Grid\tCtrl+G",
# "Toggle Grid on Plot", self.onToggleGrid)
# self.menubar.Append(pmenu, "Plot Options")
self.SetMenuBar(self.menubar)
def onAbout(self,evt):
dlg = wx.MessageDialog(self, self._about,"About Epics StepScan",
wx.OK | wx.ICON_INFORMATION)
dlg.ShowModal()
dlg.Destroy()
def onClose(self,evt):
for obj in self.plotters:
try:
obj.Destroy()
except:
pass
for nam in dir(self.larch.symtable._sys.wx):
obj = getattr(self.larch.symtable._sys.wx, nam)
del obj
self.Destroy()
def onReadScan(self, evt=None):
dlg = wx.FileDialog(self, message="Load Epics Scan Data File",
defaultDir=os.getcwd(),
wildcard=FILE_WILDCARDS, style=wx.FD_OPEN)
if dlg.ShowModal() == wx.ID_OK:
path = dlg.GetPath()
path = path.replace('\\', '/')
if path in self.filemap:
if wx.ID_YES != popup(self, "Re-read file '%s'?" % path,
'Re-read file?'):
return
gname = randname(n=5)
if hasattr(self.datagroups, gname):
time.sleep(0.005)
gname = randname(n=6)
parent, fname = os.path.split(path)
self.larch("%s = read_xdi('%s')" % (gname, path))
self.larch("%s.path = '%s'" % (gname, path))
self.filelist.Append(fname)
self.filemap[fname] = gname
print( 'Larch:: ', gname, path, fname)
self.ShowFile(filename=fname)
dlg.Destroy()
class StripChartFrame(wx.Frame):
def __init__(self, parent, ID, **kws):
kws["style"] = wx.DEFAULT_FRAME_STYLE | wx.RESIZE_BORDER | wx.TAB_TRAVERSAL
wx.Frame.__init__(self, parent, ID, '', wx.DefaultPosition,
wx.Size(-1, -1), **kws)
self.SetTitle("wxmplot StripChart Demo")
self.tmin = 15.0
self.SetFont(wx.Font(12, wx.SWISS, wx.NORMAL, wx.BOLD, False))
menu = wx.Menu()
ID_EXIT = wx.NewId()
ID_TIMER = wx.NewId()
menu_exit = menu.Append(ID_EXIT, "E&xit", "Terminate the program")
menuBar = wx.MenuBar()
menuBar.Append(menu, "&File")
self.SetMenuBar(menuBar)
self.Bind(wx.EVT_MENU, self.OnExit, menu_exit)
self.Bind(wx.EVT_CLOSE, self.OnExit)
sbar = self.CreateStatusBar(2, wx.CAPTION)
sfont = sbar.GetFont()
sfont.SetWeight(wx.BOLD)
sfont.SetPointSize(11)
sbar.SetFont(sfont)
self.SetStatusWidths([-3, -1])
self.SetStatusText('', 0)
mainsizer = wx.BoxSizer(wx.VERTICAL)
btnpanel = wx.Panel(self, -1)
btnsizer = wx.BoxSizer(wx.HORIZONTAL)
b_on = wx.Button(btnpanel, -1, 'Start', size=(-1, -1))
b_off = wx.Button(btnpanel, -1, 'Stop', size=(-1, -1))
b_on.Bind(wx.EVT_BUTTON, self.onStartTimer)
b_off.Bind(wx.EVT_BUTTON, self.onStopTimer)
tlabel = wx.StaticText(btnpanel, -1, ' Time range:')
self.time_range = FloatCtrl(btnpanel,
size=(100, -1),
value=abs(self.tmin),
precision=1)
btnsizer.Add(b_on, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER | wx.LEFT, 0)
btnsizer.Add(b_off, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER | wx.LEFT, 0)
btnsizer.Add(
tlabel, 1,
wx.GROW | wx.ALL | wx.ALIGN_LEFT | wx.ALIGN_CENTER | wx.LEFT, 0)
btnsizer.Add(self.time_range, 0,
wx.ALIGN_LEFT | wx.ALIGN_CENTER | wx.LEFT, 0)
btnpanel.SetSizer(btnsizer)
btnsizer.Fit(btnpanel)
self.plotpanel = PlotPanel(self, messenger=self.write_message)
self.plotpanel.BuildPanel()
self.plotpanel.set_xlabel('Time from Present (s)')
mainsizer.Add(btnpanel, 0,
wx.GROW | wx.ALIGN_LEFT | wx.ALIGN_CENTER | wx.LEFT, 0)
mainsizer.Add(
self.plotpanel, 1,
wx.GROW | wx.ALL | wx.ALIGN_LEFT | wx.ALIGN_CENTER | wx.LEFT, 0)
self.SetSizer(mainsizer)
mainsizer.Fit(self)
self.Bind(wx.EVT_TIMER, self.onTimer)
self.timer = wx.Timer(self)
self.count = 0
self.Refresh()
wx.CallAfter(self.onStartTimer)
def write_message(self, msg, panel=0):
"""write a message to the Status Bar"""
self.SetStatusText(msg, panel)
def onStartTimer(self, event=None):
self.count = 0
t0, y0 = next_data()
self.ylist = [y0]
self.tlist = [t0]
self.tmin_last = -10000
self.time0 = time.time()
self.timer.Start(50)
def onStopTimer(self, event=None):
self.timer.Stop()
def onTimer(self, event):
self.count += 1
etime = time.time() - self.time0
self.tmin = float(self.time_range.GetValue())
t1, y1 = next_data()
self.tlist.append(t1)
self.ylist.append(y1)
tdat = np.array(self.tlist) - t1
mask = np.where(tdat > -abs(self.tmin))
ydat = np.array(self.ylist)
n = len(self.ylist)
if n <= 2:
self.plotpanel.plot(tdat, ydat)
else:
self.plotpanel.update_line(0, tdat, ydat, draw=True)
self.write_message(" %i points in %8.4f s" % (n, etime))
lims = self.plotpanel.get_viewlimits()
try:
ymin, ymax = ydat[mask].min(), ydat[mask].max()
except:
ymin, ymax = ydat.min(), ydat.max()
tmin = max(int(min(tdat)) - 1.0, -self.tmin)
if (ymin < lims[2] or ymax > lims[3] or tmin != self.tmin_last
or time.time() - self.last_update > 2):
self.tmin_last = tmin
self.last_update = time.time()
self.plotpanel.set_xylims((tmin, 0, ymin, ymax))
def OnAbout(self, event):
dlg = wx.MessageDialog(self, "wxmplot example: stripchart app",
"About WXMPlot test",
wx.OK | wx.ICON_INFORMATION)
dlg.ShowModal()
dlg.Destroy()
def OnExit(self, event):
self.Destroy()
class Viewer1DXRD(wx.Panel):
'''
Frame for housing all 1D XRD viewer widgets
'''
label='Viewer'
def __init__(self,parent,owner=None,_larch=None):
wx.Panel.__init__(self, parent)
self.parent = parent
self.owner = owner
## Default information
self.data_name = []
self.xy_data = []
self.xy_plot = []
self.plotted_data = []
self.xy_scale = []
self.wavelength = None
self.xlabel = 'q (A^-1)'
self.xunits = ['q','d']
self.cif_name = []
self.cif_data = []
self.cif_plot = []
self.plotted_cif = []
self.x_for_zoom = None
self.Panel1DViewer()
##############################################
#### PANEL DEFINITIONS
def Panel1DViewer(self):
'''
Frame for housing all 1D XRD viewer widgets
'''
leftside = self.LeftSidePanel(self)
rightside = self.RightSidePanel(self)
panel1D = wx.BoxSizer(wx.HORIZONTAL)
panel1D.Add(leftside,flag=wx.ALL,border=10)
panel1D.Add(rightside,proportion=1,flag=wx.EXPAND|wx.ALL,border=10)
self.SetSizer(panel1D)
def Toolbox(self,panel):
'''
Frame for visual toolbox
'''
tlbx = wx.StaticBox(self,label='PLOT TOOLBOX')
vbox = wx.StaticBoxSizer(tlbx,wx.VERTICAL)
###########################
## X-Scale
hbox_xaxis = wx.BoxSizer(wx.HORIZONTAL)
ttl_xaxis = wx.StaticText(self, label='X-SCALE')
self.ch_xaxis = wx.Choice(self,choices=self.xunits)
self.ch_xaxis.Bind(wx.EVT_CHOICE, self.checkXaxis)
hbox_xaxis.Add(ttl_xaxis, flag=wx.RIGHT, border=8)
hbox_xaxis.Add(self.ch_xaxis, flag=wx.EXPAND, border=8)
vbox.Add(hbox_xaxis, flag=wx.ALL, border=10)
###########################
## Y-Scale
hbox_yaxis = wx.BoxSizer(wx.HORIZONTAL)
ttl_yaxis = wx.StaticText(self, label='Y-SCALE')
yscales = ['linear','log']
self.ch_yaxis = wx.Choice(self,choices=yscales)
self.ch_yaxis.Bind(wx.EVT_CHOICE, None)
hbox_yaxis.Add(ttl_yaxis, flag=wx.RIGHT, border=8)
hbox_yaxis.Add(self.ch_yaxis, flag=wx.EXPAND, border=8)
vbox.Add(hbox_yaxis, flag=wx.ALL, border=10)
return vbox
def DataBox(self,panel):
'''
Frame for data toolbox
'''
tlbx = wx.StaticBox(self,label='DATA TOOLBOX')
vbox = wx.StaticBoxSizer(tlbx,wx.VERTICAL)
###########################
## DATA CHOICE
self.ch_data = wx.Choice(self,choices=self.data_name)
self.ch_data.Bind(wx.EVT_CHOICE, self.onSELECT)
vbox.Add(self.ch_data, flag=wx.EXPAND|wx.ALL, border=8)
#self.ttl_data = wx.StaticText(self, label='')
#vbox.Add(self.ttl_data, flag=wx.EXPAND|wx.ALL, border=8)
###########################
# self.ck_bkgd = wx.CheckBox(self,label='BACKGROUND')
# self.ck_smth = wx.CheckBox(self,label='SMOOTHING')
#
# self.ck_bkgd.Bind(wx.EVT_CHECKBOX, None)
# self.ck_smth.Bind(wx.EVT_CHECKBOX, None)
#
# vbox.Add(self.ck_bkgd, flag=wx.ALL, border=8)
# vbox.Add(self.ck_smth, flag=wx.ALL, border=8)
###########################
## Scale
hbox_scl = wx.BoxSizer(wx.HORIZONTAL)
ttl_scl = wx.StaticText(self, label='SCALE Y TO:')
self.entr_scale = wx.TextCtrl(self,wx.TE_PROCESS_ENTER)
btn_scale = wx.Button(self,label='set')
btn_scale.Bind(wx.EVT_BUTTON, self.normalize1Ddata)
hbox_scl.Add(ttl_scl, flag=wx.RIGHT, border=8)
hbox_scl.Add(self.entr_scale, flag=wx.RIGHT, border=8)
hbox_scl.Add(btn_scale, flag=wx.RIGHT, border=8)
vbox.Add(hbox_scl, flag=wx.BOTTOM|wx.TOP, border=8)
###########################
## Hide/show and reset
hbox_btns = wx.BoxSizer(wx.HORIZONTAL)
btn_hide = wx.Button(self,label='hide')
btn_reset = wx.Button(self,label='reset')
btn_rmv = wx.Button(self,label='remove')
btn_hide.Bind(wx.EVT_BUTTON, self.hide1Ddata)
btn_reset.Bind(wx.EVT_BUTTON, self.reset1Dscale)
btn_rmv.Bind(wx.EVT_BUTTON, self.remove1Ddata)
btn_hide.Disable()
btn_rmv.Disable()
hbox_btns.Add(btn_reset, flag=wx.ALL, border=10)
hbox_btns.Add(btn_hide, flag=wx.ALL, border=10)
hbox_btns.Add(btn_rmv, flag=wx.ALL, border=10)
vbox.Add(hbox_btns, flag=wx.ALL, border=10)
return vbox
def AddPanel(self,panel):
hbox = wx.BoxSizer(wx.HORIZONTAL)
btn_data = wx.Button(panel,label='ADD NEW DATA SET')
btn_data.Bind(wx.EVT_BUTTON, self.loadXYFILE)
btn_cif = wx.Button(panel,label='ADD NEW CIF')
btn_cif.Bind(wx.EVT_BUTTON, self.loadCIF)
hbox.Add(btn_data, flag=wx.ALL, border=8)
hbox.Add(btn_cif, flag=wx.ALL, border=8)
return hbox
def LeftSidePanel(self,panel):
vbox = wx.BoxSizer(wx.VERTICAL)
plttools = self.Toolbox(self)
addbtns = self.AddPanel(self)
dattools = self.DataBox(self)
vbox.Add(plttools,flag=wx.ALL,border=10)
vbox.Add(addbtns,flag=wx.ALL,border=10)
vbox.Add(dattools,flag=wx.ALL,border=10)
return vbox
def RightSidePanel(self,panel):
vbox = wx.BoxSizer(wx.VERTICAL)
self.plot1DXRD(panel)
btnbox = self.QuickButtons(panel)
vbox.Add(self.plot1D,proportion=1,flag=wx.ALL|wx.EXPAND,border = 10)
vbox.Add(btnbox,flag=wx.ALL|wx.ALIGN_RIGHT,border = 10)
return vbox
def QuickButtons(self,panel):
buttonbox = wx.BoxSizer(wx.HORIZONTAL)
btn_img = wx.Button(panel,label='SAVE FIGURE')
btn_calib = wx.Button(panel,label='PLOT SETTINGS')
btn_integ = wx.Button(panel,label='RESET PLOT')
btn_img.Bind(wx.EVT_BUTTON, self.onSAVEfig)
btn_calib.Bind(wx.EVT_BUTTON, self.onPLOTset)
btn_integ.Bind(wx.EVT_BUTTON, self.onRESETplot)
buttonbox.Add(btn_img, flag=wx.ALL, border=8)
buttonbox.Add(btn_calib, flag=wx.ALL, border=8)
buttonbox.Add(btn_integ, flag=wx.ALL, border=8)
return buttonbox
##############################################
#### PLOTPANEL FUNCTIONS
def plot1DXRD(self,panel):
self.plot1D = PlotPanel(panel,size=(1000, 500))
self.plot1D.messenger = self.owner.write_message
## Set defaults for plotting
self.plot1D.set_ylabel('Intensity (a.u.)')
self.plot1D.cursor_mode = 'zoom'
## trying to get this functionality into our gui
## mkak 2016.11.10
# interactive_legend().show()
def onSAVEfig(self,event):
self.plot1D.save_figure()
def onPLOTset(self,event):
self.plot1D.configure()
def onRESETplot(self,event):
self.plot1D.reset_config()
##############################################
#### XRD PLOTTING FUNCTIONS
def add1Ddata(self,x,y,name=None,cif=False,wavelength=None):
plt_no = len(self.data_name)
if cif:
if name is None:
name = 'cif %i' % plt_no
else:
name = 'cif: %s' % name
else:
if name is None:
name = 'dataset %i' % plt_no
else:
name = 'data: %s' % name
if wavelength is not None:
self.addLAMBDA(wavelength)
## Add to data array lists
self.data_name.append(name)
self.xy_scale.append(max(y))
self.xy_data.extend([x,y])
## redefine x,y based on scales
self.xy_plot.extend([x,y])
## Add to plot
self.plotted_data.append(self.plot1D.oplot(x,y,label=name,show_legend=True))#,xlabel=self.xlabel))
## Use correct x-axis units
self.checkXaxis(None)
self.ch_data.Set(self.data_name)
self.ch_data.SetStringSelection(name)
## Update toolbox panel, scale all cif to 1000
if cif is True:
self.entr_scale.SetValue('1000')
self.normalize1Ddata(None)
else:
self.entr_scale.SetValue(str(self.xy_scale[plt_no]))
def addLAMBDA(self,wavelength,units='m'):
## convert to units A
if units == 'm':
self.wavelength = wavelength*1e10
elif units == 'cm':
self.wavelength = wavelength*1e8
elif units == 'mm':
self.wavelength = wavelength*1e7
elif units == 'um':
self.wavelength = wavelength*1e4
elif units == 'nm':
self.wavelength = wavelength*1e1
else: ## units 'A'
self.wavelength = wavelength
self.xunits.append(u'2\u03B8')
self.ch_xaxis.Set(self.xunits)
def normalize1Ddata(self,event):
plt_no = self.ch_data.GetSelection()
self.xy_scale[plt_no] = float(self.entr_scale.GetValue())
if self.xy_scale[plt_no] <= 0:
self.xy_scale[plt_no] = max(self.xy_data[(plt_no*2+1)])
self.entr_scale.SetValue(str(self.xy_scale[plt_no]))
y = self.xy_data[(plt_no*2+1)]
self.xy_plot[(plt_no*2+1)] = y/np.max(y) * self.xy_scale[plt_no]
self.updatePLOT()
def remove1Ddata(self,event):
## Needs pop up warning: "Do you really want to delete this data set from plotter?
## Current settings will not be saved."
## mkak 2016.11.10
plt_no = self.ch_data.GetSelection()
print('EVENTUALLY, button will remove plot: %s' % self.data_name[plt_no])
## removing name from list works... do not activate till rest is working
## mkak 2016.11.10
# self.data_name.remove(self.data_name[plt_no])
# self.ch_data.Set(self.data_name)
def hide1Ddata(self,event):
plt_no = self.ch_data.GetSelection()
print('EVENTUALLY, button will hide plot: %s' % self.data_name[plt_no])
def onSELECT(self,event):
data_str = self.ch_data.GetString(self.ch_data.GetSelection())
# self.ttl_data.SetLabel('SELECTED: %s' % data_str)
plt_no = self.ch_data.GetSelection()
self.entr_scale.SetValue(str(self.xy_scale[plt_no]))
def checkXaxis(self, event):
if self.ch_xaxis.GetSelection() == 2:
for plt_no in range(len(self.plotted_data)):
self.xy_plot[plt_no*2] = calc_q_to_2th(self.xy_data[plt_no*2],self.wavelength)
elif self.ch_xaxis.GetSelection() == 1:
for plt_no in range(len(self.plotted_data)):
self.xy_plot[plt_no*2] = calc_q_to_d(self.xy_data[plt_no*2])
else:
for plt_no in range(len(self.plotted_data)):
self.xy_plot[plt_no*2] = self.xy_data[plt_no*2]
if self.ch_xaxis.GetSelection() == 2:
self.xlabel = r'$2\Theta$'+r' $(^\circ)$'
elif self.ch_xaxis.GetSelection() == 1:
self.xlabel = 'd ($\AA$)'
else:
self.xlabel = 'q (1/$\AA$)'
self.plot1D.set_xlabel(self.xlabel)
self.updatePLOT()
def updatePLOT(self):
xmax,xmin,ymax,ymin = None,0,None,0
if len(self.plotted_data) > 0:
for plt_no in range(len(self.plotted_data)):
i = plt_no*2
j = i+1
x = self.xy_plot[i]
y = self.xy_plot[j]
if xmax is None or xmax < max(x):
xmax = max(x)
if xmin > min(x):
xmin = min(x)
if ymax is None or ymax < max(y):
ymax = max(y)
if ymin > min(y):
ymin = min(y)
self.plot1D.update_line(plt_no,x,y)
self.unzoom_all()
self.plot1D.canvas.draw()
if self.ch_xaxis.GetSelection() == 1:
xmax = 5
self.plot1D.set_xylims([xmin, xmax, ymin, ymax])
def reset1Dscale(self,event):
plt_no = self.ch_data.GetSelection()
self.xy_plot[(plt_no*2+1)] = self.xy_data[(plt_no*2+1)]
self.plot1D.update_line(plt_no,self.xy_plot[(plt_no*2)],
self.xy_plot[(plt_no*2+1)])
self.plot1D.canvas.draw()
self.unzoom_all()
self.updatePLOT()
self.xy_scale[plt_no] = max(self.xy_data[(plt_no*2+1)])
self.entr_scale.SetValue(str(self.xy_scale[plt_no]))
####### BEGIN #######
## THIS IS DIRECTLY FROM XRDDISPLAY.PY
## mkak 2016.11.11
def unzoom_all(self, event=None):
xmid, xrange, xmin, xmax = self._get1Dlims()
self._set_xview(xmin, xmax)
self.xview_range = None
def _get1Dlims(self):
xmin, xmax = self.plot1D.axes.get_xlim()
xrange = xmax-xmin
xmid = (xmax+xmin)/2.0
if self.x_for_zoom is not None:
xmid = self.x_for_zoom
return (xmid, xrange, xmin, xmax)
def _set_xview(self, x1, x2, keep_zoom=False, pan=False):
xmin,xmax = self.abs_limits()
xrange = x2-x1
x1 = max(xmin,x1)
x2 = min(xmax,x2)
if pan:
if x2 == xmax:
x1 = x2-xrange
elif x1 == xmin:
x2 = x1+xrange
if not keep_zoom:
self.x_for_zoom = (x1+x2)/2.0
self.plot1D.axes.set_xlim((x1, x2))
self.xview_range = [x1, x2]
self.plot1D.canvas.draw()
def abs_limits(self):
if len(self.data_name) > 0:
xmin, xmax = self.xy_plot[0].min(), self.xy_plot[0].max()
return xmin,xmax
####### END #######
##############################################
#### XRD FILE OPENING/SAVING
def loadXYFILE(self,event):
wildcards = 'XRD data file (*.xy)|*.xy|All files (*.*)|*.*'
dlg = wx.FileDialog(self, message='Choose 1D XRD data file',
defaultDir=os.getcwd(),
wildcard=wildcards, style=wx.FD_OPEN)
path, read = None, False
if dlg.ShowModal() == wx.ID_OK:
read = True
path = dlg.GetPath().replace('\\', '/')
dlg.Destroy()
if read:
try:
x,y = xy_file_reader(path)
self.add1Ddata(x,y,name=os.path.split(path)[-1])
except:
print('incorrect xy file format: %s' % os.path.split(path)[-1])
def saveXYFILE(self,event):
wildcards = 'XRD data file (*.xy)|*.xy|All files (*.*)|*.*'
dlg = wx.FileDialog(self, 'Save data as...',
defaultDir=os.getcwd(),
wildcard=wildcards,
style=wx.SAVE|wx.OVERWRITE_PROMPT)
path, save = None, False
if dlg.ShowModal() == wx.ID_OK:
save = True
path = dlg.GetPath().replace('\\', '/')
dlg.Destroy()
if save:
## mkak 2016.11.16
print('need to write something to save data - like pyFAI does?')
def loadCIF(self,event):
wildcards = 'XRD cifile (*.cif)|*.cif|All files (*.*)|*.*'
dlg = wx.FileDialog(self, message='Choose CIF',
defaultDir=os.getcwd(),
wildcard=wildcards, style=wx.FD_OPEN)
path, read = None, False
if dlg.ShowModal() == wx.ID_OK:
read = True
path = dlg.GetPath().replace('\\', '/')
dlg.Destroy()
if read:
cifile = os.path.split(path)[-1]
try:
cif = xu.materials.Crystal.fromCIF(path)
except:
print('incorrect file format: %s' % os.path.split(path)[-1])
return
## generate hkl list
hkllist = []
maxhkl = 8
for i in range(-maxhkl,maxhkl+1):
for j in range(-maxhkl,maxhkl+1):
for k in range(-maxhkl,maxhkl+1):
if i+j+k > 0: # as long as h,k,l all positive, eliminates 0,0,0
hkllist.append([i,j,k])
hc = constants.value(u'Planck constant in eV s') * \
constants.value(u'speed of light in vacuum') * 1e-3 ## units: keV-m
if self.wavelength is not None:
qlist = cif.Q(hkllist)
Flist = cif.StructureFactorForQ(qlist,(hc/(self.wavelength*(1e-10))*1e3))
Fall = []
qall = []
hklall = []
for i,hkl in enumerate(hkllist):
if np.abs(Flist[i]) > 0.01:
Fadd = np.abs(Flist[i])
qadd = np.linalg.norm(qlist[i])
if qadd not in qall and qadd < 6:
Fall.extend((0,Fadd,0))
qall.extend((qadd,qadd,qadd))
if np.shape(Fall)[0] > 0:
Fall = np.array(Fall)
qall = np.array(qall)
self.add1Ddata(qall,Fall,name=os.path.split(path)[-1],cif=True)
else:
print('Could not calculate real structure factors.')
else:
print('Wavelength/energy must be specified for structure factor calculations.')
def openPONI(self,event):
wildcards = 'pyFAI calibration file (*.poni)|*.poni|All files (*.*)|*.*'
dlg = wx.FileDialog(self, message='Choose pyFAI calibration file',
defaultDir=os.getcwd(),
wildcard=wildcards, style=wx.FD_OPEN)
path, read = None, False
if dlg.ShowModal() == wx.ID_OK:
read = True
path = dlg.GetPath().replace('\\', '/')
dlg.Destroy()
if read:
try:
print('Loading calibration file: %s' % path)
ai = pyFAI.load(path)
except:
print('Not recognized as a pyFAI calibration file.')
return
self.addLAMBDA(ai._wavelength,units='m')
def setLAMBDA(self,event):
dlg = SetLambdaDialog()
path, okay = None, False
if dlg.ShowModal() == wx.ID_OK:
okay = True
wavelength = dlg.wavelength
dlg.Destroy()
if okay:
self.addLAMBDA(wavelength,units='A')
class Fitting1DXRD(wx.Panel):
'''
Frame for housing all 1D XRD fitting widgets
'''
label='Fitting'
def __init__(self,parent,owner=None,_larch=None):
wx.Panel.__init__(self, parent)
self.parent = parent
self.owner = owner
## Default information
self.xlabel = 'q (A^-1)'
self.xunits = ['q','d']
self.Panel1DFitting()
##############################################
#### PANEL DEFINITIONS
def Panel1DFitting(self):
'''
Frame for housing all 1D XRD viewer widgets
'''
leftside = self.LeftSidePanel(self)
rightside = self.RightSidePanel(self)
panel1D = wx.BoxSizer(wx.HORIZONTAL)
panel1D.Add(leftside,flag=wx.ALL,border=10)
panel1D.Add(rightside,proportion=1,flag=wx.EXPAND|wx.ALL,border=10)
self.SetSizer(panel1D)
def Toolbox(self,panel):
'''
Frame for visual toolbox
'''
tlbx = wx.StaticBox(self,label='PLOT TOOLBOX')
vbox = wx.StaticBoxSizer(tlbx,wx.VERTICAL)
###########################
## X-Scale
hbox_xaxis = wx.BoxSizer(wx.HORIZONTAL)
ttl_xaxis = wx.StaticText(self, label='X-SCALE')
self.ch_xaxis = wx.Choice(self,choices=self.xunits)
self.ch_xaxis.Bind(wx.EVT_CHOICE, self.checkXaxis)
hbox_xaxis.Add(ttl_xaxis, flag=wx.RIGHT, border=8)
hbox_xaxis.Add(self.ch_xaxis, flag=wx.EXPAND, border=8)
vbox.Add(hbox_xaxis, flag=wx.ALL, border=10)
###########################
## Y-Scale
hbox_yaxis = wx.BoxSizer(wx.HORIZONTAL)
ttl_yaxis = wx.StaticText(self, label='Y-SCALE')
yscales = ['linear','log']
self.ch_yaxis = wx.Choice(self,choices=yscales)
self.ch_yaxis.Bind(wx.EVT_CHOICE, None)
hbox_yaxis.Add(ttl_yaxis, flag=wx.RIGHT, border=8)
hbox_yaxis.Add(self.ch_yaxis, flag=wx.EXPAND, border=8)
vbox.Add(hbox_yaxis, flag=wx.ALL, border=10)
return vbox
def LeftSidePanel(self,panel):
vbox = wx.BoxSizer(wx.VERTICAL)
plttools = self.Toolbox(self)
vbox.Add(plttools,flag=wx.ALL,border=10)
return vbox
def RightSidePanel(self,panel):
vbox = wx.BoxSizer(wx.VERTICAL)
self.plot1DXRD(panel)
btnbox = self.QuickButtons(panel)
vbox.Add(self.plot1D,proportion=1,flag=wx.ALL|wx.EXPAND,border = 10)
vbox.Add(btnbox,flag=wx.ALL|wx.ALIGN_RIGHT,border = 10)
return vbox
def QuickButtons(self,panel):
buttonbox = wx.BoxSizer(wx.HORIZONTAL)
btn_img = wx.Button(panel,label='SAVE FIGURE')
btn_calib = wx.Button(panel,label='PLOT SETTINGS')
btn_integ = wx.Button(panel,label='RESET PLOT')
btn_img.Bind(wx.EVT_BUTTON, self.onSAVEfig)
btn_calib.Bind(wx.EVT_BUTTON, self.onPLOTset)
btn_integ.Bind(wx.EVT_BUTTON, self.onRESETplot)
buttonbox.Add(btn_img, flag=wx.ALL, border=8)
buttonbox.Add(btn_calib, flag=wx.ALL, border=8)
buttonbox.Add(btn_integ, flag=wx.ALL, border=8)
return buttonbox
##############################################
#### PLOTPANEL FUNCTIONS
def plot1DXRD(self,panel):
self.plot1D = PlotPanel(panel,size=(1000, 500))
self.plot1D.messenger = self.owner.write_message
## Set defaults for plotting
self.plot1D.set_ylabel('Intensity (a.u.)')
self.plot1D.cursor_mode = 'zoom'
## trying to get this functionality into our gui
## mkak 2016.11.10
# interactive_legend().show()
def onSAVEfig(self,event):
self.plot1D.save_figure()
def onPLOTset(self,event):
self.plot1D.configure()
def onRESETplot(self,event):
self.plot1D.reset_config()
def checkXaxis(self, event):
if self.ch_xaxis.GetSelection() == 2:
for plt_no in range(len(self.plotted_data)):
self.xy_plot[plt_no*2] = calc_q_to_2th(self.xy_data[plt_no*2],self.wavelength)
elif self.ch_xaxis.GetSelection() == 1:
for plt_no in range(len(self.plotted_data)):
self.xy_plot[plt_no*2] = calc_q_to_d(self.xy_data[plt_no*2])
else:
for plt_no in range(len(self.plotted_data)):
self.xy_plot[plt_no*2] = self.xy_data[plt_no*2]
if self.ch_xaxis.GetSelection() == 2:
self.xlabel = r'$2\Theta$'+r' $(^\circ)$'
elif self.ch_xaxis.GetSelection() == 1:
self.xlabel = 'd ($\AA$)'
else:
self.xlabel = 'q (1/$\AA$)'
self.plot1D.set_xlabel(self.xlabel)
self.updatePLOT()
def updatePLOT(self):
xmax,xmin,ymax,ymin = None,0,None,0
if len(self.plotted_data) > 0:
for plt_no in range(len(self.plotted_data)):
i = plt_no*2
j = i+1
x = self.xy_plot[i]
y = self.xy_plot[j]
if xmax is None or xmax < max(x):
xmax = max(x)
if xmin > min(x):
xmin = min(x)
if ymax is None or ymax < max(y):
ymax = max(y)
if ymin > min(y):
ymin = min(y)
self.plot1D.update_line(plt_no,x,y)
self.unzoom_all()
self.plot1D.canvas.draw()
if self.ch_xaxis.GetSelection() == 1:
xmax = 5
self.plot1D.set_xylims([xmin, xmax, ymin, ymax])
def reset1Dscale(self,event):
plt_no = self.ch_data.GetSelection()
self.xy_plot[(plt_no*2+1)] = self.xy_data[(plt_no*2+1)]
self.plot1D.update_line(plt_no,self.xy_plot[(plt_no*2)],
self.xy_plot[(plt_no*2+1)])
self.plot1D.canvas.draw()
self.unzoom_all()
self.updatePLOT()
self.xy_scale[plt_no] = max(self.xy_data[(plt_no*2+1)])
self.entr_scale.SetValue(str(self.xy_scale[plt_no]))
####### BEGIN #######
## THIS IS DIRECTLY FROM XRDDISPLAY.PY
## mkak 2016.11.11
def unzoom_all(self, event=None):
xmid, xrange, xmin, xmax = self._get1Dlims()
self._set_xview(xmin, xmax)
self.xview_range = None
def _get1Dlims(self):
xmin, xmax = self.plot1D.axes.get_xlim()
xrange = xmax-xmin
xmid = (xmax+xmin)/2.0
if self.x_for_zoom is not None:
xmid = self.x_for_zoom
return (xmid, xrange, xmin, xmax)
def _set_xview(self, x1, x2, keep_zoom=False, pan=False):
xmin,xmax = self.abs_limits()
xrange = x2-x1
x1 = max(xmin,x1)
x2 = min(xmax,x2)
if pan:
if x2 == xmax:
x1 = x2-xrange
elif x1 == xmin:
x2 = x1+xrange
if not keep_zoom:
self.x_for_zoom = (x1+x2)/2.0
self.plot1D.axes.set_xlim((x1, x2))
self.xview_range = [x1, x2]
self.plot1D.canvas.draw()
def abs_limits(self):
if len(self.data_name) > 0:
xmin, xmax = self.xy_plot[0].min(), self.xy_plot[0].max()
return xmin,xmax
class StripChartFrame(wx.Frame):
def __init__(self, parent, ID, **kws):
kws["style"] = wx.DEFAULT_FRAME_STYLE|wx.RESIZE_BORDER|wx.TAB_TRAVERSAL
wx.Frame.__init__(self, parent, ID, '',
wx.DefaultPosition, wx.Size(-1,-1), **kws)
self.SetTitle("wxmplot StripChart Demo")
self.tmin = 15.0
self.SetFont(wx.Font(12,wx.SWISS,wx.NORMAL,wx.BOLD,False))
menu = wx.Menu()
ID_EXIT = wx.NewId()
ID_TIMER = wx.NewId()
menu_exit = menu.Append(ID_EXIT, "E&xit",
"Terminate the program")
menuBar = wx.MenuBar()
menuBar.Append(menu, "&File");
self.SetMenuBar(menuBar)
self.Bind(wx.EVT_MENU, self.OnExit, menu_exit)
self.Bind(wx.EVT_CLOSE, self.OnExit)
sbar = self.CreateStatusBar(2,wx.CAPTION)
sfont = sbar.GetFont()
sfont.SetWeight(wx.BOLD)
sfont.SetPointSize(11)
sbar.SetFont(sfont)
self.SetStatusWidths([-3,-1])
self.SetStatusText('',0)
mainsizer = wx.BoxSizer(wx.VERTICAL)
btnpanel = wx.Panel(self, -1)
btnsizer = wx.BoxSizer(wx.HORIZONTAL)
b_on = wx.Button(btnpanel, -1, 'Start', size=(-1,-1))
b_off = wx.Button(btnpanel, -1, 'Stop', size=(-1,-1))
b_on.Bind(wx.EVT_BUTTON, self.onStartTimer)
b_off.Bind(wx.EVT_BUTTON, self.onStopTimer)
tlabel = wx.StaticText(btnpanel, -1, ' Time range:')
self.time_range = FloatCtrl(btnpanel, size=(100, -1),
value=abs(self.tmin), precision=1)
btnsizer.Add(b_on, 0, wx.ALIGN_LEFT|wx.ALIGN_CENTER|wx.LEFT, 0)
btnsizer.Add(b_off, 0, wx.ALIGN_LEFT|wx.ALIGN_CENTER|wx.LEFT, 0)
btnsizer.Add(tlabel, 1, wx.GROW|wx.ALL|wx.ALIGN_LEFT|wx.ALIGN_CENTER|wx.LEFT, 0)
btnsizer.Add(self.time_range, 0, wx.ALIGN_LEFT|wx.ALIGN_CENTER|wx.LEFT, 0)
btnpanel.SetSizer(btnsizer)
btnsizer.Fit(btnpanel)
self.plotpanel = PlotPanel(self, messenger=self.write_message)
self.plotpanel.BuildPanel()
self.plotpanel.set_xlabel('Time from Present (s)')
mainsizer.Add(btnpanel, 0,
wx.GROW|wx.ALIGN_LEFT|wx.ALIGN_CENTER|wx.LEFT, 0)
mainsizer.Add(self.plotpanel, 1,
wx.GROW|wx.ALL|wx.ALIGN_LEFT|wx.ALIGN_CENTER|wx.LEFT, 0)
self.SetSizer(mainsizer)
mainsizer.Fit(self)
self.Bind(wx.EVT_TIMER, self.onTimer)
self.timer = wx.Timer(self)
self.count = 0
self.Refresh()
wx.CallAfter(self.onStartTimer)
def write_message(self, msg, panel=0):
"""write a message to the Status Bar"""
self.SetStatusText(msg, panel)
def onStartTimer(self,event=None):
self.count = 0
t0,y0 = next_data()
self.ylist = [y0]
self.tlist = [t0]
self.tmin_last = -10000
self.time0 = time.time()
self.timer.Start(50)
def onStopTimer(self,event=None):
self.timer.Stop()
def onTimer(self, event):
self.count += 1
etime = time.time() - self.time0
self.tmin = float(self.time_range.GetValue())
t1, y1 = next_data()
self.tlist.append(t1)
self.ylist.append(y1)
tdat = np.array(self.tlist) - t1
mask = np.where(tdat > -abs(self.tmin))
ydat = np.array(self.ylist)
n = len(self.ylist)
if n <= 2:
self.plotpanel.plot(tdat, ydat)
else:
self.plotpanel.update_line(0, tdat, ydat, draw=True)
self.write_message(" %i points in %8.4f s" % (n,etime))
lims = self.plotpanel.get_viewlimits()
try:
ymin, ymax = ydat[mask].min(), ydat[mask].max()
except:
ymin, ymax = ydat.min(), ydat.max()
tmin = max(int(min(tdat)) - 1.0, -self.tmin)
if (ymin < lims[2] or ymax > lims[3] or
tmin != self.tmin_last or time.time()-self.last_update > 2):
self.tmin_last = tmin
self.last_update = time.time()
self.plotpanel.set_xylims((tmin, 0, ymin, ymax))
def OnAbout(self, event):
dlg = wx.MessageDialog(self, "wxmplot example: stripchart app",
"About WXMPlot test", wx.OK | wx.ICON_INFORMATION)
dlg.ShowModal()
dlg.Destroy()
def OnExit(self, event):
self.Destroy()
class PlotterFrame(wx.Frame):
_about = """StepScan 2D Plotter
Matt Newville <newville @ cars.uchicago.edu>
"""
def __init__(self,
dbname=None,
server='sqlite',
host=None,
port=None,
user=None,
password=None,
create=True,
**kws):
wx.Frame.__init__(self, None, -1, style=FRAMESTYLE)
self.data = None
self.filemap = {}
title = "Step Scan Data File Viewer"
self.scandb = None
if dbname is not None:
self.scandb = ScanDB(dbname=dbname,
server=server,
host=host,
user=user,
password=password,
port=port,
create=create)
self.filemap[CURSCAN] = SCANGROUP
title = '%s, with Live Scan Viewing' % title
self.larch = None
self.plotters = []
self.SetTitle(title)
self.SetSize((850, 650))
self.SetFont(Font(9))
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)
if dbname is not None:
self.live_scanfile = None
self.live_cpt = -1
self.filelist.Append(CURSCAN)
self.scantimer = wx.Timer(self)
self.Bind(wx.EVT_TIMER, self.onScanTimer, self.scantimer)
self.scantimer.Start(250)
def onScanTimer(self, evt=None, **kws):
if self.larch is None:
return
group = getattr(self.larch.symtable, SCANGROUP)
curfile = fix_filename(self.scandb.get_info('filename'))
if curfile != self.live_scanfile:
self.live_scanfile = curfile
group.filename = self.live_scanfile
group.array_units = []
self.live_cpt = -1
sdata = self.scandb.get_scandata()
if len(sdata) <= 1:
return
npts = len(sdata[-1].data)
if npts <= self.live_cpt:
return
self.live_cpt = npts
if len(group.array_units) < 1:
group.array_units = [str(row.notes) for row in sdata]
for row in sdata:
setattr(group, fix_filename(row.name), np.array(row.data))
if npts > 1:
self.onPlot()
def createMainPanel(self):
splitter = wx.SplitterWindow(self, style=wx.SP_LIVE_UPDATE)
splitter.SetMinimumPaneSize(175)
self.filelist = wx.ListBox(splitter)
self.filelist.SetBackgroundColour(wx.Colour(255, 255, 255))
self.filelist.Bind(wx.EVT_LISTBOX, self.ShowFile)
self.detailspanel = self.createDetailsPanel(splitter)
splitter.SplitVertically(self.filelist, self.detailspanel, 1)
wx.CallAfter(self.init_larch)
def createDetailsPanel(self, parent):
mainpanel = wx.Panel(parent)
mainsizer = wx.BoxSizer(wx.VERTICAL)
panel = wx.Panel(mainpanel)
sizer = wx.GridBagSizer(8, 7)
self.title = SimpleText(panel, 'initializing...')
ir = 0
sizer.Add(self.title, (ir, 0), (1, 6), LCEN, 2)
# x-axis
self.xarr = add_choice(panel,
choices=[],
action=self.onYchoice,
size=(120, -1))
self.xop = add_choice(panel,
choices=('', 'log'),
action=self.onYchoice,
size=(75, -1))
ir += 1
sizer.Add(SimpleText(panel, 'X = '), (ir, 0), (1, 1), CEN, 0)
sizer.Add(self.xop, (ir, 1), (1, 1), CEN, 0)
sizer.Add(SimpleText(panel, '('), (ir, 2), (1, 1), CEN, 0)
sizer.Add(self.xarr, (ir, 3), (1, 1), RCEN, 0)
sizer.Add(SimpleText(panel, ')'), (ir, 4), (1, 1), CEN, 0)
self.yops = [[], []]
self.yarr = [[], []]
for opts, sel, siz in ((PRE_OPS, 0, 75), (ARR_OPS, 3, 50), (ARR_OPS, 3,
50)):
w1 = add_choice(panel,
choices=opts,
action=self.onYchoice,
size=(siz, -1))
w1.SetSelection(sel)
self.yops[0].append(w1)
w2 = add_choice(panel,
choices=opts,
action=self.onYchoice,
size=(siz, -1))
w2.SetSelection(sel)
self.yops[1].append(w2)
opts = {'choices': [], 'size': (120, -1), 'action': self.onYchoice}
for i in range(3):
self.yarr[0].append(add_choice(panel, **opts))
self.yarr[1].append(add_choice(panel, **opts))
for i in range(2):
ir += 1
label = 'Y%i = ' % (i + 1)
sizer.Add(SimpleText(panel, label), (ir, 0), (1, 1), CEN, 0)
sizer.Add(self.yops[i][0], (ir, 1), (1, 1), CEN, 0)
sizer.Add(SimpleText(panel, '[('), (ir, 2), (1, 1), CEN, 0)
sizer.Add(self.yarr[i][0], (ir, 3), (1, 1), CEN, 0)
sizer.Add(self.yops[i][1], (ir, 4), (1, 1), CEN, 0)
sizer.Add(self.yarr[i][1], (ir, 5), (1, 1), CEN, 0)
sizer.Add(SimpleText(panel, ')'), (ir, 6), (1, 1), LCEN, 0)
sizer.Add(self.yops[i][2], (ir, 7), (1, 1), CEN, 0)
sizer.Add(self.yarr[i][2], (ir, 8), (1, 1), CEN, 0)
sizer.Add(SimpleText(panel, ']'), (ir, 9), (1, 1), LCEN, 0)
ir += 1
# sizer.Add(SimpleText(panel, ' New Plot: '), (ir, 0), (1, 3), LCEN, 0)
# sizer.Add(SimpleText(panel, ' Over Plot: '), (ir+1, 0), (1, 3), LCEN, 0)
for jr, ic, dc, opt, ttl in ((0, 0, 4, 'win old',
'New Plot, This Window'),
(0, 4, 2, 'win new',
'New Plot, New Window'),
(1, 0, 4, 'over left',
'Over Plot, Left Axis'),
(1, 4, 2, 'over right',
'Over Plot, Right Axis')):
sizer.Add(
add_button(panel,
ttl,
size=(165, -1),
action=Closure(self.onPlot, opt=opt)),
(ir + jr, ic), (1, dc), LCEN, 2)
ir += 2
self.dtcorr = check(panel, default=True, label='correct deadtime?')
sizer.Add(self.dtcorr, (ir, 0), (1, 3), LCEN, 0)
ir += 1
sizer.Add(SimpleText(panel, ''), (ir, 0), (1, 3), LCEN, 0)
pack(panel, sizer)
# self.nb = flat_nb.FlatNotebook(mainpanel, -1, agwStyle=FNB_STYLE)
#
# self.nb.SetTabAreaColour(wx.Colour(248,248,240))
# self.nb.SetActiveTabColour(wx.Colour(254,254,195))
#
# self.nb.SetNonActiveTabTextColour(wx.Colour(40,40,180))
# self.nb.SetActiveTabTextColour(wx.Colour(80,0,0))
#
# self.xas_panel = self.CreateXASPanel(self.nb) # mainpanel)
# self.fit_panel = self.CreateFitPanel(self.nb) # mainpanel)
#
# self.nb.AddPage(self.fit_panel, ' General Analysis ', True)
# self.nb.AddPage(self.xas_panel, ' XAS Processing ', True)
mainsizer.Add(panel, 0, LCEN | wx.EXPAND, 2)
self.plotpanel = PlotPanel(mainpanel, size=(500, 670))
self.plotpanel.messenger = self.write_message
bgcol = panel.GetBackgroundColour()
bgcol = (bgcol[0] / 255., bgcol[1] / 255., bgcol[2] / 255.)
self.plotpanel.canvas.figure.set_facecolor(bgcol)
mainsizer.Add(self.plotpanel, 1, wx.GROW | wx.ALL, 1)
# mainsizer.Add(self.nb, 1, LCEN|wx.EXPAND, 2)
pack(mainpanel, mainsizer)
return mainpanel
def CreateFitPanel(self, parent):
p = panel = wx.Panel(parent)
self.fit_model = add_choice(panel,
size=(100, -1),
choices=('Gaussian', 'Lorentzian', 'Voigt',
'Linear', 'Quadratic', 'Step',
'Rectangle', 'Exponential'))
self.fit_bkg = add_choice(panel,
size=(100, -1),
choices=('None', 'constant', 'linear',
'quadtratic'))
self.fit_step = add_choice(panel,
size=(100, -1),
choices=('linear', 'error function',
'arctan'))
self.fit_report = wx.StaticText(panel, -1, "", (180, 200))
sizer = wx.GridBagSizer(10, 4)
sizer.Add(SimpleText(p, 'Fit Model: '), (0, 0), (1, 1), LCEN)
sizer.Add(self.fit_model, (0, 1), (1, 1), LCEN)
sizer.Add(SimpleText(p, 'Background: '), (1, 0), (1, 1), LCEN)
sizer.Add(self.fit_bkg, (1, 1), (1, 1), LCEN)
sizer.Add(SimpleText(p, 'Step Function Form: '), (2, 0), (1, 1), LCEN)
sizer.Add(self.fit_step, (2, 1), (1, 1), LCEN)
sizer.Add(
add_button(panel,
'Show Fit',
size=(100, -1),
action=self.onFitPeak), (3, 0), (1, 1), LCEN)
sizer.Add(self.fit_report, (0, 2), (4, 2), LCEN, 3)
pack(panel, sizer)
return panel
def CreateXASPanel(self, parent):
p = panel = wx.Panel(parent)
self.xas_autoe0 = check(panel, default=True, label='auto?')
self.xas_autostep = check(panel, default=True, label='auto?')
self.xas_op = add_choice(panel,
size=(95, -1),
choices=('Raw Data', 'Pre-edged',
'Normalized', 'Flattened'))
self.xas_e0 = FloatCtrl(panel, value=0, precision=3, size=(95, -1))
self.xas_step = FloatCtrl(panel, value=0, precision=3, size=(95, -1))
self.xas_pre1 = FloatCtrl(panel,
value=-200,
precision=1,
size=(95, -1))
self.xas_pre2 = FloatCtrl(panel, value=-30, precision=1, size=(95, -1))
self.xas_nor1 = FloatCtrl(panel, value=30, precision=1, size=(95, -1))
self.xas_nor2 = FloatCtrl(panel, value=300, precision=1, size=(95, -1))
self.xas_vict = add_choice(panel,
size=(50, -1),
choices=('0', '1', '2', '3'))
self.xas_nnor = add_choice(panel,
size=(50, -1),
choices=('0', '1', '2', '3'))
self.xas_vict.SetSelection(1)
self.xas_nnor.SetSelection(2)
sizer = wx.GridBagSizer(10, 4)
sizer.Add(SimpleText(p, 'Plot XAS as: '), (0, 0), (1, 1), LCEN)
sizer.Add(SimpleText(p, 'E0 : '), (1, 0), (1, 1), LCEN)
sizer.Add(SimpleText(p, 'Edge Step: '), (2, 0), (1, 1), LCEN)
sizer.Add(SimpleText(p, 'Pre-edge range: '), (3, 0), (1, 1), LCEN)
sizer.Add(SimpleText(p, 'Normalization range: '), (4, 0), (1, 1), LCEN)
sizer.Add(self.xas_op, (0, 1), (1, 1), LCEN)
sizer.Add(self.xas_e0, (1, 1), (1, 1), LCEN)
sizer.Add(self.xas_step, (2, 1), (1, 1), LCEN)
sizer.Add(self.xas_pre1, (3, 1), (1, 1), LCEN)
sizer.Add(SimpleText(p, ':'), (3, 2), (1, 1), LCEN)
sizer.Add(self.xas_pre2, (3, 3), (1, 1), LCEN)
sizer.Add(self.xas_nor1, (4, 1), (1, 1), LCEN)
sizer.Add(SimpleText(p, ':'), (4, 2), (1, 1), LCEN)
sizer.Add(self.xas_nor2, (4, 3), (1, 1), LCEN)
sizer.Add(self.xas_autoe0, (1, 2), (1, 2), LCEN)
sizer.Add(self.xas_autostep, (2, 2), (1, 2), LCEN)
sizer.Add(SimpleText(p, 'Victoreen:'), (3, 4), (1, 1), LCEN)
sizer.Add(self.xas_vict, (3, 5), (1, 1), LCEN)
sizer.Add(SimpleText(p, 'PolyOrder:'), (4, 4), (1, 1), LCEN)
sizer.Add(self.xas_nnor, (4, 5), (1, 1), LCEN)
pack(panel, sizer)
return panel
def onFitPeak(self, evt=None):
gname = self.groupname
if self.dtcorr.IsChecked():
print('fit needs to dt correct!')
dtext = []
model = self.fit_model.GetStringSelection().lower()
dtext.append('Fit Model: %s' % model)
bkg = self.fit_bkg.GetStringSelection()
if bkg == 'None':
bkg = None
if bkg is None:
dtext.append('No Background')
else:
dtext.append('Background: %s' % bkg)
step = self.fit_step.GetStringSelection().lower()
if model in ('step', 'rectangle'):
dtext.append('Step form: %s' % step)
lgroup = getattr(self.larch.symtable, gname)
x = lgroup._x1_
y = lgroup._y1_
pgroup = fit_peak(x,
y,
model,
background=bkg,
step=step,
_larch=self.larch)
text = fit_report(pgroup.params, _larch=self.larch)
dtext.append('Parameters: ')
for pname in dir(pgroup.params):
par = getattr(pgroup.params, pname)
if isParameter(par):
ptxt = " %s= %.4f" % (par.name, par.value)
if (hasattr(par, 'stderr') and par.stderr is not None):
ptxt = "%s(%.4f)" % (ptxt, par.stderr)
dtext.append(ptxt)
dtext = '\n'.join(dtext)
# plotframe = self.get_plotwindow()
# plotframe.oplot(x, pgroup.fit, label='fit (%s)' % model)
text = fit_report(pgroup.params, _larch=self.larch)
self.fit_report.SetLabel(dtext)
def xas_process(self, gname, plotopts):
""" process (pre-edge/normalize) XAS data from XAS form, overwriting
larch group '_y1_' attribute to be plotted
"""
out = self.xas_op.GetStringSelection().lower() # raw, pre, norm, flat
if out.startswith('raw'):
return plotopts
preopts = {'group': gname, 'e0': None, 'step': None}
lgroup = getattr(self.larch.symtable, gname)
if self.dtcorr.IsChecked():
print('need to dt correct!')
if not self.xas_autoe0.IsChecked():
xmin, xmax = min(lgroup._x1_), max(lgroup._x1_)
e0 = self.xas_e0.GetValue()
if e0 < xmax and e0 > xmin:
preopts['e0'] = e0
if not self.xas_autostep.IsChecked():
preopts['step'] = self.xas_step.GetValue()
preopts['pre1'] = self.xas_pre1.GetValue()
preopts['pre2'] = self.xas_pre2.GetValue()
preopts['norm1'] = self.xas_nor1.GetValue()
preopts['norm2'] = self.xas_nor2.GetValue()
preopts['nvict'] = self.xas_vict.GetSelection()
preopts['nnorm'] = self.xas_nnor.GetSelection()
preopts = ", ".join(["%s=%s" % (k, v) for k, v in preopts.items()])
preedge_cmd = "pre_edge(%s._x1_, %s._y1_, %s)" % (gname, gname,
preopts)
self.larch(preedge_cmd)
self.xas_e0.SetValue(lgroup.e0)
self.xas_step.SetValue(lgroup.edge_step)
if out.startswith('pre'):
self.larch('%s._y1_ = %s.norm * %s.edge_step' %
(gname, gname, gname))
elif out.startswith('norm'):
self.larch('%s._y1_ = %s.norm' % (gname, gname))
elif out.startswith('flat'):
self.larch('%s._y1_ = %s.flat' % (gname, gname))
return plotopts
def init_larch(self):
t0 = time.time()
from larch.wxlib import inputhook
self.larch = Interpreter()
self.larch.symtable.set_symbol('_sys.wx.wxapp', wx.GetApp())
self.larch.symtable.set_symbol('_sys.wx.parent', self)
self.larch('%s = group(filename="%s")' % (SCANGROUP, CURSCAN))
self.SetStatusText('ready')
self.datagroups = self.larch.symtable
self.title.SetLabel('')
def write_message(self, s, panel=0):
"""write a message to the Status Bar"""
self.SetStatusText(s, panel)
def get_plotwindow(self, new=False, **kws):
pframe = None
if not new:
while pframe is None:
try:
pframe = self.plotters.pop()
pframe.Show()
pframe.Raise()
except IndexError:
pframe = None
break
except PyDeadObjectError:
pframe = None
if pframe is None:
pframe = PlotFrame()
pframe.Show()
pframe.Raise()
self.plotters.append(pframe)
return pframe
def onYchoice(self, evt=None, side='left'):
self.onPlot()
def onPlot(self, evt=None, opt='new old', npts=None):
# 'win new', 'New Window'),
# 'win old', 'Old Window'),
# 'over left', 'Left Axis'),
# 'over right', 'Right Axis')):
# 'update left', from scan
optwords = opt.split()
# plotframe = self.get_plotwindow(new=('new' in optwords[1]))
# plotcmd = plotframe.plot
plotcmd = self.plotpanel.plot
optwords = opt.split()
side = 'left'
update = False
if optwords[0] == 'over':
side = optwords[1]
plotcmd = self.plotpanel.oplot
elif optwords[0] == 'update' and npts > 4:
plotcmd = self.plotpanel.update_line
update = True
popts = {'side': side}
ix = self.xarr.GetSelection()
x = self.xarr.GetStringSelection()
try:
gname = self.groupname
lgroup = getattr(self.larch.symtable, gname)
except:
gname = SCANGROUP
lgroup = getattr(self.larch.symtable, gname)
xfmt = "%s._x1_ = %s(%s)"
yfmt = "%s._y1_ = %s((%s %s %s) %s (%s))"
xop = self.xop.GetStringSelection()
xlabel = x
try:
xunits = lgroup.array_units[ix]
except:
xunits = ''
if xop != '':
xlabel = "%s(%s)" % (xop, xlabel)
if xunits != '':
xlabel = '%s (%s)' % (xlabel, xunits)
popts['xlabel'] = xlabel
opl1 = self.yops[0][0].GetStringSelection()
opl2 = self.yops[0][1].GetStringSelection()
opl3 = self.yops[0][2].GetStringSelection()
yl1 = self.yarr[0][0].GetStringSelection()
yl2 = self.yarr[0][1].GetStringSelection()
yl3 = self.yarr[0][2].GetStringSelection()
opr1 = self.yops[1][0].GetStringSelection()
opr2 = self.yops[1][1].GetStringSelection()
opr3 = self.yops[1][2].GetStringSelection()
yr1 = self.yarr[1][0].GetStringSelection()
yr2 = self.yarr[1][1].GetStringSelection()
yr3 = self.yarr[1][2].GetStringSelection()
ylabel = yl1
if yl2 == '':
yl2, opl2 = '1', '*'
else:
ylabel = "%s%s%s" % (ylabel, opl2, yl2)
if yl3 == '':
yl3, opl3 = '1', '*'
else:
ylabel = "(%s)%s%s" % (ylabel, opl3, yl3)
if opl1 != '':
ylabel = "%s(%s)" % (opl1, ylabel)
if yl1 not in ('0', '1'): yl1 = "%s.%s" % (gname, yl1)
if yl2 not in ('0', '1'): yl2 = "%s.%s" % (gname, yl2)
if yl3 not in ('0', '1'): yl3 = "%s.%s" % (gname, yl3)
if x not in ('0', '1'): x = "%s.%s" % (gname, x)
self.larch(xfmt % (gname, xop, x))
self.larch(yfmt % (gname, opl1, yl1, opl2, yl2, opl3, yl3))
try:
npts = min(len(lgroup._x1_), len(lgroup._y1_))
except AttributeError:
return
lgroup._x1_ = np.array(lgroup._x1_[:npts])
lgroup._y1_ = np.array(lgroup._y1_[:npts])
path, fname = os.path.split(lgroup.filename)
popts['label'] = "%s: %s" % (fname, ylabel)
if side == 'right':
popts['y2label'] = ylabel
else:
popts['ylabel'] = ylabel
if plotcmd == self.plotpanel.plot:
popts['title'] = fname
# XAFS Processing!
#if (self.nb.GetCurrentPage() == self.xas_panel):
# popts = self.xas_process(gname, popts)
if update:
self.plotpanel.set_xlabel(popts['xlabel'])
self.plotpanel.set_ylabel(popts['ylabel'])
plotcmd(0, lgroup._x1_, lgroup._y1_, draw=True,
update_limits=True) # ((npts < 5) or (npts % 5 == 0)))
self.plotpanel.set_xylims((min(lgroup._x1_), max(lgroup._x1_),
min(lgroup._y1_), max(lgroup._y1_)))
else:
plotcmd(lgroup._x1_, lgroup._y1_, **popts)
self.plotpanel.canvas.draw()
def ShowFile(self, evt=None, filename=None, **kws):
if filename is None and evt is not None:
filename = evt.GetString()
key = filename
if filename in self.filemap:
key = self.filemap[filename]
if key == SCANGROUP:
array_labels = [
fix_filename(s.name) for s in self.scandb.get_scandata()
]
title = filename
elif hasattr(self.datagroups, key):
data = getattr(self.datagroups, key)
title = data.filename
array_labels = data.array_labels[:]
self.groupname = key
xcols = array_labels[:]
ycols = array_labels[:]
y2cols = array_labels[:] + ['1.0', '0.0', '']
ncols = len(xcols)
self.title.SetLabel(title)
self.xarr.SetItems(xcols)
self.xarr.SetSelection(0)
self.xop.SetSelection(0)
for i in range(2):
for j in range(3):
self.yarr[i][j].SetItems(y2cols)
self.yarr[i][j].SetSelection(len(y2cols))
if i == 0:
self.yarr[i][0].SetItems(ycols)
self.yarr[i][0].SetSelection(1)
inb = 0
for colname in xcols:
if 'energ' in colname.lower():
inb = 1
#self.nb.SetSelection(inb)
def createMenus(self):
# ppnl = self.plotpanel
self.menubar = wx.MenuBar()
#
fmenu = wx.Menu()
pmenu = wx.Menu()
add_menu(self, fmenu, "&Open Scan File\tCtrl+O", "Read Scan File",
self.onReadScan)
fmenu.AppendSeparator()
add_menu(self, fmenu, "&Quit\tCtrl+Q", "Quit program", self.onClose)
self.menubar.Append(fmenu, "&File")
# fmenu.AppendSeparator()
# add_menu(self, fmenu, "&Copy\tCtrl+C",
# "Copy Figure to Clipboard", self.onClipboard)
# add_menu(self, fmenu, "&Save\tCtrl+S", "Save Figure", self.onSaveFig)
# add_menu(self, fmenu, "&Print\tCtrl+P", "Print Figure", self.onPrint)
# add_menu(self, fmenu, "Page Setup", "Print Page Setup", self.onPrintSetup)
# add_menu(self, fmenu, "Preview", "Print Preview", self.onPrintPreview)
#
# add_menu(self, pmenu, "Configure\tCtrl+K",
# "Configure Plot", self.onConfigurePlot)
#add_menu(self, pmenu, "Unzoom\tCtrl+Z", "Unzoom Plot", self.onUnzoom)
##pmenu.AppendSeparator()
#add_menu(self, pmenu, "Toggle Legend\tCtrl+L",
# "Toggle Legend on Plot", self.onToggleLegend)
#add_menu(self, pmenu, "Toggle Grid\tCtrl+G",
# "Toggle Grid on Plot", self.onToggleGrid)
# self.menubar.Append(pmenu, "Plot Options")
self.SetMenuBar(self.menubar)
def onAbout(self, evt):
dlg = wx.MessageDialog(self, self._about, "About Epics StepScan",
wx.OK | wx.ICON_INFORMATION)
dlg.ShowModal()
dlg.Destroy()
def onClose(self, evt):
for obj in self.plotters:
try:
obj.Destroy()
except:
pass
for nam in dir(self.larch.symtable._sys.wx):
obj = getattr(self.larch.symtable._sys.wx, nam)
del obj
self.Destroy()
def onReadScan(self, evt=None):
dlg = wx.FileDialog(self,
message="Load Epics Scan Data File",
defaultDir=os.getcwd(),
wildcard=FILE_WILDCARDS,
style=wx.FD_OPEN)
if dlg.ShowModal() == wx.ID_OK:
path = dlg.GetPath()
path = path.replace('\\', '/')
if path in self.filemap:
if wx.ID_YES != popup(self, "Re-read file '%s'?" % path,
'Re-read file?'):
return
gname = randname(n=5)
if hasattr(self.datagroups, gname):
time.sleep(0.005)
gname = randname(n=6)
parent, fname = os.path.split(path)
self.larch("%s = read_xdi('%s')" % (gname, path))
self.larch("%s.path = '%s'" % (gname, path))
self.filelist.Append(fname)
self.filemap[fname] = gname
print('Larch:: ', gname, path, fname)
self.ShowFile(filename=fname)
dlg.Destroy()
