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