class XYFitController():
"""
class hollding the Larch session and doing the
processing work for Larch XYFit
"""
config_file = 'xyfit.conf'
def __init__(self, wxparent=None, _larch=None):
self.wxparent = wxparent
self.larch = _larch
if self.larch is None:
self.larch = Interpreter()
self.filelist = None
self.file_groups = {}
self.proc_opts = {}
self.fit_opts = {}
self.group = None
self.groupname = None
self.report_frame = None
self.symtable = self.larch.symtable
self.symtable.set_symbol('_sys.wx.wxapp', wx.GetApp())
self.symtable.set_symbol('_sys.wx.parent', self)
def init_larch(self):
fico = self.get_iconfile()
_larch = self.larch
_larch.eval("import xafs_plots")
_larch.symtable._sys.xyfit = Group()
config = read_config(self.config_file)
if (config is None or 'workdir' not in config or
'data_proc' not in config or 'xas_proc' not in config):
config = self.make_default_config()
for key, value in config.items():
setattr(_larch.symtable._sys.xyfit, key, value)
os.chdir(config['workdir'])
def make_default_config(self):
""" default config, probably called on first run of program"""
config = {'chdir_on_fileopen': True,
'workdir': os.getcwd()}
config['data_proc'] = dict(xshift=0, xscale=1, yshift=0,
yscale=1, smooth_op='None',
smooth_conv='Lorentzian',
smooth_c0=2, smooth_c1=1,
smooth_sig=1)
config['xas_proc'] = dict(e0=0, pre1=-200, pre2=-10,
edge_step=0, nnorm=2, norm1=25,
norm2=-10, nvict=1, auto_step=True,
auto_e0=True, show_e0=True,
xas_op='Normalized')
return config
def get_config(self, key, default=None):
"get configuration setting"
confgroup = self.larch.symtable._sys.xyfit
return getattr(confgroup, key, default)
def save_config(self):
"""save configuration"""
conf = group2dict(self.larch.symtable._sys.xyfit)
conf.pop('__name__')
save_config(self.config_file, conf)
def set_workdir(self):
self.larch.symtable._sys.xyfit.workdir = os.getcwd()
def show_report(self, text, evt=None):
shown = False
try:
self.report_frame.Raise()
shown = True
except:
del self.report_frame
if not shown:
self.report_frame = ReportFrame(self.wxparent)
self.report_frame.SetFont(Font(8))
self.report_frame.set_text(text)
self.report_frame.SetFont(Font(8))
self.report_frame.Raise()
def get_iconfile(self):
larchdir = self.symtable._sys.config.larchdir
return os.path.join(larchdir, 'icons', ICON_FILE)
def get_display(self, stacked=False):
win = 1
wintitle='Larch XYFit Array Plot Window'
if stacked:
win = 2
wintitle='Larch XYFit Fit Plot Window'
opts = dict(wintitle=wintitle, stacked=stacked, win=win)
out = self.symtable._plotter.get_display(**opts)
return out
def get_group(self, groupname):
if groupname is None:
groupname = self.groupname
grp = getattr(self.symtable, groupname, None)
if not hasattr(grp, 'proc_opts'):
grp.proc_opts = {}
return grp
def get_proc_opts(self, dgroup):
opts = {}
opts.update(self.get_config('data_proc', default={}))
if dgroup.datatype == 'xas':
opts.update(self.get_config('xas_proc', {}))
if hasattr(dgroup, 'proc_opts'):
opts.update(dgroup.proc_opts)
return opts
def process(self, dgroup, proc_opts=None):
if not hasattr(dgroup, 'proc_opts'):
dgroup.proc_opts = {}
if 'xscale' not in dgroup.proc_opts:
dgroup.proc_opts.update(self.get_proc_opts(dgroup))
if proc_opts is not None:
dgroup.proc_opts.update(proc_opts)
opts = {'group': dgroup.groupname}
opts.update(dgroup.proc_opts)
# scaling
cmds = []
cmds.append("{group:s}.x = {xscale:f}*({group:s}.xdat + {xshift:f})")
cmds.append("{group:s}.y = {yscale:f}*({group:s}.ydat + {yshift:f})")
# smoothing
smop = opts['smooth_op'].lower()
smcmd = None
if smop.startswith('box'):
opts['smooth_c0'] = int(opts['smooth_c0'])
smcmd = "boxcar({group:s}.y, {smooth_c0:d})"
elif smop.startswith('savit'):
opts['smooth_c0'] = int(opts['smooth_c0'])
opts['smooth_c1'] = int(opts['smooth_c1'])
smcmd = "savitzky_golay({group:s}.y, {smooth_c0:d}, {smooth_c1:d})"
elif smop.startswith('conv'):
cform = str(opts['smooth_conv'].lower())
smcmd = "smooth({group:s}.x, {group:s}.y, sigma={smooth_sig:f}, form='{smooth_conv:s}')"
if smcmd is not None:
cmds.append("{group:s}.y = " + smcmd)
for cmd in cmds:
self.larch.eval(cmd.format(**opts))
# xas
if dgroup.datatype.startswith('xas'):
dgroup.energy = dgroup.x*1.0
dgroup.mu = dgroup.y*1.0
copts = [dgroup.groupname]
if not opts['auto_e0']:
_e0 = opts['e0']
if _e0 < max(dgroup.energy) and _e0 > min(dgroup.energy):
copts.append("e0=%.4f" % float(_e0))
if not opts['auto_step']:
copts.append("step=%.4f" % opts['edge_step'])
for attr in ('pre1', 'pre2', 'nvict', 'nnorm', 'norm1', 'norm2'):
copts.append("%s=%.4f" % (attr, opts[attr]))
self.larch.eval("pre_edge(%s)" % (','.join(copts)))
opts['e0'] = dgroup.e0
opts['edge_step'] = dgroup.edge_step
for attr in ('pre1', 'pre2', 'norm1', 'norm2'):
opts[attr] = getattr(dgroup.pre_edge_details, attr)
dgroup.proc_opts.update(opts)
def get_cursor(self):
try:
xval = self.symtable._plotter.plot1_x
yval = self.symtable._plotter.plot1_y
except:
xval, yval = None, None
return xval, yval
def plot_group(self, groupname=None, title=None, new=True, **kws):
ppanel = self.get_display(stacked=False).panel
newplot = ppanel.plot
oplot = ppanel.oplot
plotcmd = oplot
if new:
plotcmd = newplot
dgroup = self.get_group(groupname)
if not hasattr(dgroup, 'xdat'):
print("Cannot plot group ", groupname)
if dgroup.datatype == 'xas':
if ((getattr(dgroup, 'plot_yarrays', None) is None or
getattr(dgroup, 'energy', None) is None or
getattr(dgroup, 'mu', None) is None)):
# print("-> Mode.process")
self.process(dgroup)
if not hasattr(dgroup, 'x'):
dgroup.x = dgroup.xdat[:]
if not hasattr(dgroup, 'y'):
dgroup.y = dgroup.ydat[:]
if hasattr(dgroup, 'plot_yarrays'):
plot_yarrays = dgroup.plot_yarrays
else:
plot_yarrays = [(dgroup.y, {}, None)]
popts = kws
path, fname = os.path.split(dgroup.filename)
if not 'label' in popts:
popts['label'] = dgroup.plot_ylabel
popts['xlabel'] = dgroup.plot_xlabel
popts['ylabel'] = dgroup.plot_ylabel
if getattr(dgroup, 'plot_y2label', None) is not None:
popts['y2label'] = dgroup.plot_y2label
plot_ymarkers = None
if new:
if title is None:
title = fname
plot_ymarkers = getattr(dgroup, 'plot_ymarkers', None)
popts['title'] = title
for yarr in plot_yarrays:
popts.update(yarr[1])
if popts['label'] is None and yarr[2] is not None:
popts['label'] = yarr[2]
plotcmd(dgroup.x, yarr[0], **popts)
plotcmd = oplot
if plot_ymarkers is not None:
axes = ppanel.axes
for x, y, opts in plot_ymarkers:
popts = {'marker': 'o', 'markersize': 4,
'markerfacecolor': 'red', 'label': '',
'markeredgecolor': 'black'}
popts.update(opts)
axes.plot([x], [y], **popts)
ppanel.canvas.draw()
class XASController():
"""
class hollding the Larch session and doing the
processing work for Larch XAS GUI
"""
config_file = 'xas_viewer.conf'
def __init__(self, wxparent=None, _larch=None):
self.wxparent = wxparent
self.larch = _larch
if self.larch is None:
self.larch = Interpreter()
self.filelist = None
self.file_groups = OrderedDict()
self.fit_opts = {}
self.group = None
self.groupname = None
self.report_frame = None
self.symtable = self.larch.symtable
def init_larch(self):
fico = self.get_iconfile()
_larch = self.larch
_larch.eval(XASGUI_STARTUP)
old_config = read_config(self.config_file)
config = self.make_default_config()
for sname in config:
if old_config is not None and sname in old_config:
val = old_config[sname]
if isinstance(val, dict):
config[sname].update(val)
else:
config[sname] = val
for key, value in config.items():
setattr(_larch.symtable._sys.xas_viewer, key, value)
os.chdir(config['workdir'])
def make_default_config(self):
""" default config, probably called on first run of program"""
config = {'chdir_on_fileopen': True, 'workdir': os.getcwd()}
return config
def get_config(self, key, default=None):
"get configuration setting"
confgroup = self.larch.symtable._sys.xas_viewer
return getattr(confgroup, key, default)
def save_config(self):
"""save configuration"""
conf = group2dict(self.larch.symtable._sys.xas_viewer)
conf.pop('__name__')
save_config(self.config_file, conf)
def set_workdir(self):
self.larch.symtable._sys.xas_viewer.workdir = os.getcwd()
def show_report(self, fitresult, evt=None):
shown = False
try:
self.report_frame.Raise()
shown = True
except:
del self.report_frame
if not shown:
self.report_frame = ReportFrame(self.wxparent)
model_repr = fitresult.model._reprstring(long=True)
report = fit_report(fitresult,
show_correl=True,
min_correl=0.25,
sort_pars=True)
self.report_frame.SetFont(Font(FONTSIZE - 1))
self.report_frame.set_text(report)
self.report_frame.SetFont(Font(FONTSIZE - 1))
self.report_frame.Raise()
def get_iconfile(self):
larchdir = self.symtable._sys.config.larchdir
return os.path.join(larchdir, 'icons', ICON_FILE)
def get_display(self, win=1, stacked=False):
wintitle = 'Larch XAS Plot Window %i' % win
# if stacked:
# win = 2
# wintitle='Larch XAS Plot Window'
opts = dict(wintitle=wintitle,
stacked=stacked,
win=win,
size=PLOTWIN_SIZE)
out = self.symtable._plotter.get_display(**opts)
if win > 1:
p1 = getattr(self.symtable._plotter, 'plot1', None)
if p1 is not None:
try:
siz = p1.GetSize()
pos = p1.GetPosition()
pos[0] += int(siz[0] / 4)
pos[1] += int(siz[1] / 4)
out.SetSize(pos)
if not stacked:
out.SetSize(siz)
except Exception:
pass
return out
def get_group(self, groupname=None):
if groupname is None:
groupname = self.groupname
if groupname is None:
return None
dgroup = getattr(self.symtable, groupname, None)
if dgroup is None and groupname in self.file_groups:
groupname = self.file_groups[groupname]
dgroup = getattr(self.symtable, groupname, None)
return dgroup
def merge_groups(self, grouplist, master=None, yarray='mu', outgroup=None):
"""merge groups"""
cmd = """%s = merge_groups(%s, master=%s,
xarray='energy', yarray='%s', kind='cubic', trim=True)"""
glist = "[%s]" % (', '.join(grouplist))
outgroup = fix_varname(outgroup.lower())
if outgroup is None:
outgroup = 'merged'
outgroup = unique_name(outgroup, self.file_groups, max=1000)
cmd = cmd % (outgroup, glist, master, yarray)
self.larch.eval(cmd)
if master is None:
master = grouplist[0]
this = self.get_group(outgroup)
master = self.get_group(master)
if not hasattr(this, 'xasnorm_config'):
this.xasnorm_config = {}
this.xasnorm_config.update(master.xasnorm_config)
this.datatype = master.datatype
this.xdat = 1.0 * this.energy
this.ydat = 1.0 * getattr(this, yarray)
this.plot_xlabel = 'energy'
this.plot_ylabel = yarray
return outgroup
def copy_group(self, filename, new_filename=None):
"""copy XAS group (by filename) to new group"""
groupname = self.file_groups[filename]
if not hasattr(self.larch.symtable, groupname):
return
ogroup = self.get_group(groupname)
ngroup = Group(datatype=ogroup.datatype, copied_from=groupname)
for attr in dir(ogroup):
do_copy = True
if attr in ('xdat', 'ydat', 'i0', 'data' 'yerr', 'energy', 'mu'):
val = getattr(ogroup, attr) * 1.0
elif attr in ('norm', 'flat', 'deriv', 'deconv', 'post_edge',
'pre_edge'):
do_copy = False
else:
try:
val = copy.deepcopy(getattr(ogroup, attr))
except ValueError:
do_copy = False
if do_copy:
setattr(ngroup, attr, val)
if new_filename is None:
new_filename = filename + '_1'
ngroup.filename = unique_name(new_filename, self.file_groups.keys())
ngroup.groupname = unique_name(groupname, self.file_groups.values())
setattr(self.larch.symtable, ngroup.groupname, ngroup)
return ngroup
def get_cursor(self, win=None):
"""get last cursor from selected window"""
return last_cursor_pos(win=win, _larch=self.larch)
def plot_group(self,
groupname=None,
title=None,
plot_yarrays=None,
new=True,
zoom_out=True,
**kws):
ppanel = self.get_display(stacked=False).panel
newplot = ppanel.plot
oplot = ppanel.oplot
plotcmd = oplot
viewlims = ppanel.get_viewlimits()
if new:
plotcmd = newplot
dgroup = self.get_group(groupname)
if not hasattr(dgroup, 'xdat'):
print("Cannot plot group ", groupname)
if ((getattr(dgroup, 'plot_yarrays', None) is None
or getattr(dgroup, 'energy', None) is None
or getattr(dgroup, 'mu', None) is None)):
self.process(dgroup)
if plot_yarrays is None and hasattr(dgroup, 'plot_yarrays'):
plot_yarrays = dgroup.plot_yarrays
popts = kws
path, fname = os.path.split(dgroup.filename)
if not 'label' in popts:
popts['label'] = dgroup.plot_ylabel
zoom_out = (zoom_out or min(dgroup.xdat) >= viewlims[1]
or max(dgroup.xdat) <= viewlims[0]
or min(dgroup.ydat) >= viewlims[3]
or max(dgroup.ydat) <= viewlims[2])
if not zoom_out:
popts['xmin'] = viewlims[0]
popts['xmax'] = viewlims[1]
popts['ymin'] = viewlims[2]
popts['ymax'] = viewlims[3]
popts['xlabel'] = dgroup.plot_xlabel
popts['ylabel'] = dgroup.plot_ylabel
if getattr(dgroup, 'plot_y2label', None) is not None:
popts['y2label'] = dgroup.plot_y2label
plot_extras = None
if new:
if title is None:
title = fname
plot_extras = getattr(dgroup, 'plot_extras', None)
popts['title'] = title
if hasattr(dgroup, 'custom_plotopts'):
popts.update(dgroup.custom_plotopts)
narr = len(plot_yarrays) - 1
for i, pydat in enumerate(plot_yarrays):
yaname, yopts, yalabel = pydat
popts.update(yopts)
if yalabel is not None:
popts['label'] = yalabel
popts['delay_draw'] = (i != narr)
plotcmd(dgroup.xdat, getattr(dgroup, yaname), **popts)
plotcmd = oplot
if plot_extras is not None:
axes = ppanel.axes
for etype, x, y, opts in plot_extras:
if etype == 'marker':
popts = {
'marker': 'o',
'markersize': 4,
'label': '_nolegend_',
'markerfacecolor': 'red',
'markeredgecolor': '#884444'
}
popts.update(opts)
axes.plot([x], [y], **popts)
elif etype == 'vline':
popts = {'ymin': 0, 'ymax': 1.0, 'color': '#888888'}
popts.update(opts)
axes.axvline(x, **popts)
ppanel.canvas.draw()
class XYFitController():
"""
class hollding the Larch session and doing the
processing work for Larch XYFit
"""
def __init__(self, wxparent=None, _larch=None):
self.wxparent = wxparent
self.larch = _larch
if self.larch is None:
self.larch = Interpreter()
self.filelist = None
self.file_groups = {}
self.proc_opts = {}
self.fit_opts = {}
self.group = None
self.groupname = None
self.report_frame = None
self.symtable = self.larch.symtable
self.symtable.set_symbol('_sys.wx.wxapp', wx.GetApp())
self.symtable.set_symbol('_sys.wx.parent', self)
def show_report(self, text, evt=None):
shown = False
try:
self.report_frame.Raise()
shown = True
except:
del self.report_frame
if not shown:
self.report_frame = ReportFrame(self.wxparent)
self.report_frame.SetFont(Font(8))
self.report_frame.set_text(text)
self.report_frame.SetFont(Font(8))
self.report_frame.Raise()
def get_iconfile(self):
larchdir = self.symtable._sys.config.larchdir
return os.path.join(larchdir, 'icons', ICON_FILE)
def get_display(self, stacked=False):
win = 1
wintitle = 'Larch XYFit Array Plot Window'
if stacked:
win = 2
wintitle = 'Larch XYFit Fit Plot Window'
opts = dict(wintitle=wintitle, stacked=stacked, win=win)
out = self.symtable._plotter.get_display(**opts)
return out
def get_group(self, groupname):
if groupname is None:
groupname = self.groupname
grp = getattr(self.symtable, groupname, None)
if not hasattr(grp, 'proc_opts'):
grp.proc_opts = {}
return grp
def get_proc_opts(self, dgroup):
opts = dict(xshift=0,
xscale=1,
yshift=0,
yscale=1,
smooth_op='None',
smooth_conv='Lorentzian',
smooth_c0=2,
smooth_c1=1,
smooth_sig=1)
if dgroup.datatype == 'xas':
opts.update(
dict(e0=0,
pre1=-200,
pre2=-30,
edge_step=0,
nnorm=3,
norm1=50,
norm2=-10,
nvict=2,
auto_step=True,
auto_e0=True,
show_e0=True,
xas_op='Raw Data'))
if hasattr(dgroup, 'proc_opts'):
opts.update(dgroup.proc_opts)
return opts
def process(self, dgroup, proc_opts=None):
if not hasattr(dgroup, 'proc_opts'):
dgroup.proc_opts = {}
if 'xscale' not in dgroup.proc_opts:
dgroup.proc_opts.update(self.get_proc_opts(dgroup))
if proc_opts is not None:
dgroup.proc_opts.update(proc_opts)
opts = {'group': dgroup.groupname}
opts.update(dgroup.proc_opts)
# scaling
cmds = [
"{group:s}.x = {xscale:f}*({group:s}.xdat + {xshift:f})",
"{group:s}.y = {yscale:f}*({group:s}.ydat + {yshift:f})"
]
# smoothing
smop = opts['smooth_op'].lower()
smcmd = None
if smop.startswith('box'):
opts['smooth_c0'] = int(opts['smooth_c0'])
smcmd = "boxcar({group:s}.y, {smooth_c0:d})"
elif smop.startswith('savit'):
opts['smooth_c0'] = int(opts['smooth_c0'])
opts['smooth_c1'] = int(opts['smooth_c1'])
smcmd = "savitzky_golay({group:s}.y, {smooth_c0:d}, {smooth_c1:d})"
elif smop.startswith('conv'):
cform = str(opts['smooth_conv'].lower())
smcmd = "smooth({group:s}.x, {group:s}.y, sigma={smooth_sig:f}, form='{smooth_conv:s}')"
if smcmd is not None:
cmds.append("{group:s}.y = " + smcmd)
for cmd in cmds:
self.larch.eval(cmd.format(**opts))
# xas
if dgroup.datatype.startswith('xas'):
dgroup.energy = dgroup.x
dgroup.mu = dgroup.y
popts = dict(group=dgroup.groupname,
e0='None',
step='None',
make_flat='False')
if not opts['auto_e0']:
_e0 = opts['e0']
if _e0 < max(dgroup.energy) and _e0 > min(dgroup.energy):
popts['e0'] = "%.f" % float(_e0)
if not opts['auto_step']:
popts['step'] = "%.f" % opts['step']
for attr in ('pre1', 'pre2', 'nvict', 'nnorm', 'norm1', 'norm2'):
popts[attr] = "%.f" % opts[attr]
cmd = """pre_edge({group:s}, e0={e0:s}, step={step:s}, pre1={pre1:s}, pre2={pre2:s},
norm1={norm1:s}, norm2={norm2:s}, nnorm={nnorm:s}, nvict={nvict:s})""".format(
**popts)
self.larch.eval(cmd)
for attr in ('e0', 'edge_step'):
opts[attr] = getattr(dgroup, attr)
for attr in ('pre1', 'pre2', 'norm1', 'norm2'):
opts[attr] = getattr(dgroup.pre_edge_details, attr)
dgroup.proc_opts.update(opts)
def get_cursor(self):
try:
xval = self.symtable._plotter.plot1_x
yval = self.symtable._plotter.plot1_y
except:
xval, yval = None, None
return xval, yval
def plot_group(self, groupname=None, title=None, new=True, **kws):
ppanel = self.get_display(stacked=False).panel
newplot = ppanel.plot
oplot = ppanel.oplot
plotcmd = oplot
if new:
plotcmd = newplot
dgroup = self.get_group(groupname)
if not hasattr(dgroup, 'xdat'):
print("Cannot plot group ", groupname)
if dgroup.datatype == 'xas':
if ((getattr(dgroup, 'plot_yarrays', None) is None
or getattr(dgroup, 'energy', None) is None
or getattr(dgroup, 'mu', None) is None)):
# print("-> Mode.process")
self.process(dgroup)
if not hasattr(dgroup, 'x'):
dgroup.x = dgroup.xdat[:]
if not hasattr(dgroup, 'y'):
dgroup.y = dgroup.ydat[:]
if hasattr(dgroup, 'plot_yarrays'):
plot_yarrays = dgroup.plot_yarrays
else:
plot_yarrays = [(dgroup.y, {}, None)]
popts = kws
path, fname = os.path.split(dgroup.filename)
if not 'label' in popts:
popts['label'] = "%s: %s" % (fname, dgroup.plot_ylabel)
popts['xlabel'] = dgroup.plot_xlabel
popts['ylabel'] = dgroup.plot_ylabel
if getattr(dgroup, 'plot_y2label', None) is not None:
popts['y2label'] = dgroup.plot_y2label
if plotcmd == newplot and title is None:
title = fname
popts['title'] = title
for yarr in plot_yarrays:
popts.update(yarr[1])
if yarr[2] is not None:
popts['label'] = yarr[2]
plotcmd(dgroup.x, yarr[0], **popts)
plotcmd = oplot
if hasattr(dgroup, 'plot_ymarkers'):
axes = ppanel.axes
for x, y, opts in dgroup.plot_ymarkers:
popts = {
'marker': 'o',
'markersize': 4,
'markerfacecolor': 'red',
'markeredgecolor': 'black'
}
popts.update(opts)
axes.plot([x], [y], **popts)
ppanel.canvas.draw()