class ScanViewerFrame(wx.Frame):
_about = """Scan Viewer, Matt Newville <newville @ cars.uchicago.edu> """
TIME_MSG = 'Point %i/%i, Time Remaining ~ %s '
def __init__(self, parent, dbname=None, server='sqlite', host=None,
port=None, user=None, password=None, create=True, **kws):
wx.Frame.__init__(self, None, -1, style=FRAMESTYLE)
title = "Epics Step Scan Viewer"
self.parent = parent
self.scandb = getattr(parent, 'scandb', None)
if self.scandb is None and dbname is not None:
self.scandb = ScanDB(dbname=dbname, server=server, host=host,
user=user, password=password, port=port,
create=create)
self.larch = None
self.lgroup = None
self.SetTitle(title)
self.SetSize((750, 750))
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 self.scandb is not None:
self.get_info = self.scandb.get_info
self.scandb_server = self.scandb.server
self.live_scanfile = None
self.live_cpt = -1
self.total_npts = 1
self.scantimer = wx.Timer(self)
self.Bind(wx.EVT_TIMER, self.onScanTimer, self.scantimer)
self.scantimer.Start(50)
self.Show()
self.Raise()
def onScanTimer(self, evt=None, **kws):
if self.lgroup is None:
return
curfile = fix_filename(self.get_info('filename'))
sdata = self.scandb.get_scandata()
npts = len(sdata[-1].data)
if (npts > 2 and npts == self.live_cpt and
curfile == self.live_scanfile): # no new data
return
# filename changed -- scan starting, so update
# list of positioners, detectors, etc
force_newplot = False
if curfile != self.live_scanfile:
force_newplot = True
self.live_scanfile = curfile
self.title.SetLabel(curfile)
self.set_column_names(sdata)
if npts == self.live_cpt:
return
time_est = hms(self.get_info('scan_time_estimate', as_int=True))
msg = self.TIME_MSG % (npts, self.total_npts, time_est)
self.SetStatusText(msg)
self.live_cpt = npts
for row in sdata:
dat = row.data
if self.scandb_server == 'sqlite':
dat = json.loads(dat.replace('{', '[').replace('}', ']'))
setattr(self.lgroup, fix_varname(row.name), np.array(dat))
if npts > 1:
self.onPlot(npts=npts, force_newplot=force_newplot)
def set_column_names(self, sdata):
"""set column names from values read from scandata table"""
self.lgroup.array_units = [fix_varname(s.units) for s in sdata]
self.total_npts = self.get_info('scan_total_points', as_int=True)
self.live_cpt = -1
xcols, ycols, y2cols = [], [], []
for s in sdata:
nam = fix_varname(s.name)
ycols.append(nam)
if s.notes.lower().startswith('pos'):
xcols.append(nam)
y2cols = ycols[:] + ['1.0', '0.0', '']
xarr_old = self.xarr.GetStringSelection()
self.xarr.SetItems(xcols)
ix = xcols.index(xarr_old) if xarr_old in xcols else 0
self.xarr.SetSelection(ix)
for i in range(2):
for j in range(3):
yold = self.yarr[i][j].GetStringSelection()
idef, cols = 0, y2cols
if i == 0 and j == 0:
idef, cols = 1, ycols
self.yarr[i][j].SetItems(cols)
iy = cols.index(yold) if yold in cols else idef
self.yarr[i][j].SetSelection(iy)
def createMainPanel(self):
wx.CallAfter(self.init_larch)
mainpanel = wx.Panel(self)
mainsizer = wx.BoxSizer(wx.VERTICAL)
panel = wx.Panel(mainpanel)
self.yops = [[],[]]
self.yarr = [[],[]]
arr_kws= {'choices':[], 'size':(120, -1), 'action':self.onPlot}
self.title = SimpleText(panel, 'initializing...',
font=Font(13), colour='#880000')
self.xarr = add_choice(panel, **arr_kws)
for i in range(3):
self.yarr[0].append(add_choice(panel, **arr_kws))
self.yarr[1].append(add_choice(panel, **arr_kws))
for opts, sel, wid in ((PRE_OPS, 0, 100), (ARR_OPS, 3, 60),
(ARR_OPS, 3, 60)):
arr_kws['choices'] = opts
arr_kws['size'] = (wid, -1)
self.yops[0].append(add_choice(panel, default=sel, **arr_kws))
self.yops[1].append(add_choice(panel, default=sel, **arr_kws))
# place widgets
sizer = wx.GridBagSizer(5, 10)
sizer.Add(self.title, (0, 1), (1, 6), LCEN, 2)
sizer.Add(SimpleText(panel, ' X ='), (1, 0), (1, 1), CEN, 0)
sizer.Add(self.xarr, (1, 3), (1, 1), RCEN, 0)
ir = 1
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(hline(panel), (ir, 0), (1, 12), CEN|wx.GROW|wx.ALL, 0)
pack(panel, sizer)
self.plotpanel = PlotPanel(mainpanel, size=(520, 550),
axissize=(0.18, 0.18, 0.70, 0.70),
fontsize=8)
self.plotpanel.messenger = self.write_message
self.plotpanel.canvas.figure.set_facecolor((0.98,0.98,0.97))
btnsizer = wx.StdDialogButtonSizer()
btnpanel = wx.Panel(mainpanel)
btnsizer.Add(add_button(btnpanel, 'Pause', action=self.onPause))
btnsizer.Add(add_button(btnpanel, 'Resume', action=self.onResume))
btnsizer.Add(add_button(btnpanel, 'Abort', action=self.onAbort))
pack(btnpanel, btnsizer)
mainsizer.Add(panel, 0, LCEN|wx.EXPAND, 2)
mainsizer.Add(self.plotpanel, 1, wx.GROW|wx.ALL, 1)
mainsizer.Add(btnpanel, 0, wx.GROW|wx.ALL, 1)
pack(mainpanel, mainsizer)
return mainpanel
def onPause(self, evt=None):
self.scandb.set_info('request_command_pause', 1)
def onResume(self, evt=None):
self.scandb.set_info('request_command_pause', 0)
def onAbort(self, evt=None):
self.scandb.set_info('request_command_abort', 1)
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.arr_x
y = lgroup.arr_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)
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
"""
print 'Process XAS ', gname
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.arr_x), max(lgroup.arr_x)
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.larch('_sys.localGroup = %s)' % (SCANGROUP))
self.lgroup = getattr(self.larch.symtable, SCANGROUP)
self.SetStatusText('ready')
self.title.SetLabel('')
def write_message(self, s, panel=0):
"""write a message to the Status Bar"""
self.SetStatusText(s, panel)
def onPlot(self, evt=None, npts=None, force_newplot=False):
"""drow plot of newest data"""
new_plot = force_newplot or npts < 3
lgroup, gname = self.lgroup, SCANGROUP
ix = self.xarr.GetSelection()
x = self.xarr.GetStringSelection()
xlabel = x
popts = {'labelfontsize': 8, 'xlabel': x}
try:
xunits = lgroup.array_units[ix]
xlabel = '%s (%s)' % (xlabel, xunits)
except:
pass
def make_array(wids, iy):
gn = SCANGROUP
op1 = self.yops[iy][0].GetStringSelection()
op2 = self.yops[iy][1].GetStringSelection()
op3 = self.yops[iy][2].GetStringSelection()
yy1 = self.yarr[iy][0].GetStringSelection()
yy2 = self.yarr[iy][1].GetStringSelection()
yy3 = self.yarr[iy][2].GetStringSelection()
if yy1 in ('0', '1', '', None) or len(yy1) < 0:
return '', ''
label = yy1
expr = "%s.%s" % (gn, yy1)
if yy2 != '':
label = "%s%s%s" % (label, op2, yy2)
expr = "%s%s%s.%s" % (expr, op2, gn, yy2)
if yy3 != '':
label = "(%s)%s%s" % (label, op3, yy3)
expr = "(%s)%s%s.%s" % (expr, op3, gn, yy3)
if op1 != '':
label = "%s(%s)" % (op1, label)
expr = "%s(%s)" % (op1, expr)
return label, expr
ylabel, yexpr = make_array(self.yops, 0)
if yexpr == '':
return
self.larch("%s.arr_x = %s.%s" % (gname, gname, x))
self.larch("%s.arr_y1 = %s" % (gname, yexpr))
# print 'onPlot Show Groups ', lgroup
# print ' : ', dir(lgroup)
# print ' X -> ', x, lgroup.arr_x
# print ' Y -> ', yexpr, lgroup.arr_y1
try:
npts = min(len(lgroup.arr_x), len(lgroup.arr_y1))
except AttributeError:
return
y2label, y2expr = make_array(self.yops, 1)
if y2expr != '':
self.larch("%s.arr_y2 = %s" % (gname, y2expr))
n2pts = npts
try:
n2pts = min(len(lgroup.arr_x), len(lgroup.arr_y1),
len(lgroup.arr_y2))
lgroup.arr_y2 = np.array( lgroup.arr_y2[:n2pts])
except:
y2expr = ''
npts = n2pts
lgroup.arr_y1 = np.array( lgroup.arr_y1[:npts])
lgroup.arr_x = np.array( lgroup.arr_x[:npts])
path, fname = os.path.split(self.live_scanfile)
popts.update({'title': fname, 'xlabel': xlabel,
'ylabel': ylabel, 'y2label': y2label})
ppnl = self.plotpanel
if new_plot:
ppnl.plot(lgroup.arr_x, lgroup.arr_y1,
label= "%s: %s" % (fname, ylabel), **popts)
if y2expr != '':
ppnl.oplot(lgroup.arr_x, lgroup.arr_y2, side='right',
label= "%s: %s" % (fname, y2label), **popts)
ppnl.canvas.draw()
else:
ppnl.set_xlabel(xlabel)
ppnl.set_ylabel(ylabel)
ppnl.update_line(0, lgroup.arr_x, lgroup.arr_y1,
draw=True, update_limits=True)
ppnl.set_xylims((min(lgroup.arr_x), max(lgroup.arr_x),
min(lgroup.arr_y1), max(lgroup.arr_y1)))
if y2expr != '':
ppnl.set_y2label(y2label)
ppnl.update_line(1, lgroup.arr_x, lgroup.arr_y2, side='right',
draw=True, update_limits=True)
ppnl.set_xylims((min(lgroup.arr_x), max(lgroup.arr_x),
min(lgroup.arr_y2), max(lgroup.arr_y2)),
side='right')
def createMenus(self):
self.menubar = wx.MenuBar()
#
fmenu = wx.Menu()
pmenu = wx.Menu()
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 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 onClipboard(self, evt=None):
self.plotpanel.canvas.Copy_to_Clipboard(evt)
def onSaveFig(self, evt=None):
self.plotpanel.save_figure(event=evt,
transparent=True, dpi=300)
def onPrint(self, evt=None):
self.plotpanel.Print(evet)
def onPrintSetup(self, evt=None):
self.plotpanel.PrintSetup(evt)
def onPrintPreview(self, evt=None):
self.plotpanel.PrintPreview(evt)
def onConfigurePlot(self, evt=None):
self.plotpanel.configure(evt)
def onUnzoom(self, evt=None):
self.plotpanel.unzoom(evt)
def onToggleLegend(self, evt=None):
self.plotpanel.toggle_legend(evt)
def onToggleGrid(self, evt=None):
self.plotpanel.toggle_grid(evt)
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()
