def Xml2Fit_v1(self, fitElement, calibration=None):
"""
Creates a fit object from information found in a xml file
"""
# <fit>
success = True
peakModel = fitElement.get("peakModel")
bgElement = fitElement.find("background")
# Simple fix for older xml file versions, where the only background
# model was a polynomial, and therefore it did not have to be stored
try:
backgroundModel = bgElement.get("backgroundModel")
except AttributeError:
backgroundModel = "polynomial"
if backgroundModel is None:
backgroundModel = "polynomial"
fitter = Fitter(peakModel, backgroundModel)
fit = Fit(fitter, cal=calibration)
try:
fit.chi = float(fitElement.get("chi"))
except ValueError:
fit.chi = None
# <bgMarker>
for bgElement in fitElement.findall("bgMarker"):
# Read begin marker
beginElement = bgElement.find("begin")
begin = self._getPosFromElement(beginElement, fit)
fit.ChangeMarker("bg", begin, "set")
# Read end marker
endElement = bgElement.find("end")
end = self._getPosFromElement(endElement, fit)
fit.ChangeMarker("bg", end, "set")
# <regionMarker>
for regionElement in fitElement.findall("regionMarker"):
# Read begin marker
beginElement = regionElement.find("begin")
begin = self._getPosFromElement(beginElement, fit)
fit.ChangeMarker("region", begin, "set")
# Read end marker
endElement = regionElement.find("end")
end = self._getPosFromElement(endElement, fit)
fit.ChangeMarker("region", end, "set")
# <peakMarker>
for peakElement in fitElement.findall("peakMarker"):
# Read position marker
posElement = peakElement.find("position")
pos = self._getPosFromElement(posElement, fit)
fit.ChangeMarker("peak", pos, "set")
# <background>
bgElement = fitElement.find("background")
if bgElement:
try:
fit.bgChi = float(bgElement.get("chisquare"))
except ValueError:
pass
params = list()
# Distinguish between old notation of background parameters (coeff, ncoeff),
# which interprets the parameters as coefficients of a polynomial, and the
# new notation (params, npar), which interprets them as arbitrary parameters.
paramCounterName = 'npar'
paramElements = bgElement.findall('param')
if not paramElements:
paramElements = bgElement.findall('coeff')
paramCounterName = 'deg'
for paramElement in paramElements:
npar = int(paramElement.get(paramCounterName))
# <value>
valueElement = paramElement.find("value")
value = float(valueElement.text)
# <error>
errorElement = paramElement.find("error")
error = float(errorElement.text)
param = ufloat(value, error)
params.append([npar, param])
params.sort()
fit.bgParams = [p[1] for p in params]
# <peak>
statusdict = dict()
for peakElement in fitElement.findall("peak"):
# <uncal>
uncalElement = peakElement.find("uncal")
parameter = dict()
for paramElement in uncalElement:
# parameter value/error
name = paramElement.tag
parameter[name] = self._readParamElement(paramElement)
# parameter status
status = paramElement.get("status", "free")
try:
statusdict[name].append(status)
except KeyError:
statusdict[name] = [status]
# <extras>
extraElement = peakElement.find("extras")
extras = dict()
if extraElement is not None:
for paramElement in extraElement:
name = paramElement.tag
if len(paramElement) == 1:
extras[name] = paramElement.text
else:
# <value>
valueElement = paramElement.find("value")
value = float(valueElement.text)
# <error>
errorElement = paramElement.find("error")
error = float(errorElement.text)
extras[name] = ufloat(value, error)
# create peak
try:
peak = fit.fitter.peakModel.Peak(cal=calibration, **parameter)
except TypeError:
hdtv.ui.error("Error reading peak with parameters: %s" %
str(parameter))
success = False
continue
peak.extras = extras
fit.peaks.append(peak)
# set parameter status of fitter
for name in list(statusdict.keys()):
# check if status is the same for all peaks
check = set(statusdict[name])
if len(check) == 1:
status = statusdict[name][0]
else:
status = statusdict[name]
fitter.SetParameter(name, status)
integrals = dict()
for integral in fitElement.findall('integral'):
integral_type = integral.get("integraltype")
integrals[integral_type] = dict()
for calElement in integral:
cal_type = calElement.tag
integrals[integral_type][cal_type] = dict()
for paramElement in calElement:
# <value>
valueElement = paramElement.find("value")
value = float(valueElement.text)
# <error>
errorElement = paramElement.find("error")
error = float(errorElement.text)
coeff = ufloat(value, error)
integrals[integral_type][cal_type][
paramElement.tag] = coeff
if not integrals:
integrals = None
for integral_type in ['sub', 'bg']:
if integrals and not integral_type in integrals:
integrals[integral_type] = None
fit.integral = integrals
return (fit, success)
def RestoreFromXml_v0(self, root, do_fit=False):
"""
Reads fits from xml file (version = 0.*)
Note: For performance reasons this does not reconstruct the fit results.
It only sets the markers and restores the status of the fitter. The user
must repeat the fit, if he/she wants to see the results again.
(This should be improved in later versions.)
"""
count = 0
spectra = self.spectra
# <spectrum>
for specElement in root.iter():
name = specElement.get("name")
# find this spectrum from Element in the real world
spec = None
for sid in spectra.ids:
if spectra.dict[sid].name == name:
spec = spectra.dict[sid]
# maybe the spectrum that is referred to in XML is currently not
# loaded
if spec is None:
continue
# <fit>
for fitElement in specElement:
count = count + 1
peakModel = fitElement.get("peakModel")
# Simple fix for older xml file versions, where the only background
# model was a polynomial, and therefore it did not have to be stored
fitter = Fitter(peakModel, "polynomial")
# <result>
params = dict()
for resultElement in fitElement.findall("result"):
for paramElement in resultElement:
parname = paramElement.tag
status = paramElement.get("status")
try:
params[parname].append(status)
except KeyError:
params[parname] = [status]
for parname in list(params.keys()):
status = params[parname]
fitter.SetParameter(parname, status)
fit = Fit(fitter, cal=spec.cal)
# <background>
for bgElement in fitElement.findall("background"):
# Read begin/p1 marker
beginElement = bgElement.find("begin")
if beginElement is None: # Maybe old Element (ver 0.1)
beginElement = bgElement.find("p1")
begin = float(beginElement.find("uncal").text)
fit.ChangeMarker("bg", fit.cal.Ch2E(begin), "set")
# Read end/p2 marker
endElement = bgElement.find("end")
if endElement is None: # Maybe old Element (ver 0.1)
endElement = bgElement.find("p2")
end = float(endElement.find("uncal").text)
fit.ChangeMarker("bg", fit.cal.Ch2E(end), "set")
# <region>
for regionElement in fitElement.findall("region"):
# Read begin/p1 marker
beginElement = regionElement.find("begin")
if beginElement is None: # Maybe old Element (ver 0.1)
beginElement = regionElement.find("p1")
begin = float(beginElement.find("uncal").text)
fit.ChangeMarker("region", fit.cal.Ch2E(begin), "set")
# Read end/p2 marker
endElement = regionElement.find("end")
if endElement is None: # Maybe old Element (ver 0.1)
endElement = regionElement.find("p2")
end = float(endElement.find("uncal").text)
fit.ChangeMarker("region", fit.cal.Ch2E(end), "set")
# <peak>
for peakElement in fitElement.findall("peak"):
# Read position/p1 marker
posElement = peakElement.find("position")
if posElement is None:
posElement = peakElement.find("p1")
pos = float(posElement.find("uncal").text)
fit.ChangeMarker("peak", fit.cal.Ch2E(pos), "set")
if do_fit:
fit.FitPeakFunc(spec)
spec.Insert(fit)
return count, [fit]
def Xml2Fit_v1(self, fitElement, calibration=None):
"""
Creates a fit object from information found in a xml file
"""
# <fit>
success = True
peakModel = fitElement.get("peakModel")
bgdeg = int(fitElement.get("bgDegree"))
fitter = Fitter(peakModel, bgdeg)
fit = Fit(fitter, cal=calibration)
try:
fit.chi = float(fitElement.get("chi"))
except ValueError:
fit.chi = None
# <bgMarker>
for bgElement in fitElement.findall("bgMarker"):
# Read begin marker
beginElement = bgElement.find("begin")
begin = self._getPosFromElement(beginElement, fit)
fit.ChangeMarker("bg", begin, "set")
# Read end marker
endElement = bgElement.find("end")
end = self._getPosFromElement(endElement, fit)
fit.ChangeMarker("bg", end, "set")
# <regionMarker>
for regionElement in fitElement.findall("regionMarker"):
# Read begin marker
beginElement = regionElement.find("begin")
begin = self._getPosFromElement(beginElement, fit)
fit.ChangeMarker("region", begin, "set")
# Read end marker
endElement = regionElement.find("end")
end = self._getPosFromElement(endElement, fit)
fit.ChangeMarker("region", end, "set")
# <peakMarker>
for peakElement in fitElement.findall("peakMarker"):
# Read position marker
posElement = peakElement.find("position")
pos = self._getPosFromElement(posElement, fit)
fit.ChangeMarker("peak", pos, "set")
# <background>
bgElement = fitElement.find("background")
if bgElement:
try:
fit.bgChi = float(bgElement.get("chisquare"))
except ValueError:
pass
coeffs = list()
for coeffElement in bgElement.findall("coeff"):
deg = int(coeffElement.get("deg"))
# <value>
valueElement = coeffElement.find("value")
value = float(valueElement.text)
# <error>
errorElement = coeffElement.find("error")
error = float(errorElement.text)
coeff = ufloat(value, error)
coeffs.append([deg, coeff])
coeffs.sort()
fit.bgCoeffs = [c[1] for c in coeffs]
# <peak>
statusdict = dict()
for peakElement in fitElement.findall("peak"):
# <uncal>
uncalElement = peakElement.find("uncal")
parameter = dict()
for paramElement in uncalElement:
# parameter value/error
name = paramElement.tag
parameter[name] = self._readParamElement(paramElement)
# parameter status
status = paramElement.get("status", "free")
try:
statusdict[name].append(status)
except KeyError:
statusdict[name] = [status]
# <extras>
extraElement = peakElement.find("extras")
extras = dict()
if extraElement is not None:
for paramElement in extraElement:
name = paramElement.tag
if len(paramElement) == 1:
extras[name] = paramElement.text
else:
# <value>
valueElement = paramElement.find("value")
value = float(valueElement.text)
# <error>
errorElement = paramElement.find("error")
error = float(errorElement.text)
extras[name] = ufloat(value, error)
# create peak
try:
peak = fit.fitter.peakModel.Peak(cal=calibration, **parameter)
except TypeError:
hdtv.ui.error(
"Error reading peak with parameters: %s" % str(parameter))
success = False
continue
peak.extras = extras
fit.peaks.append(peak)
# set parameter status of fitter
for name in list(statusdict.keys()):
# check if status is the same for all peaks
check = set(statusdict[name])
if len(check) == 1:
status = statusdict[name][0]
else:
status = statusdict[name]
fitter.SetParameter(name, status)
integrals = dict()
for integral in fitElement.findall('integral'):
integral_type = integral.get("integraltype")
integrals[integral_type] = dict()
for calElement in integral:
cal_type = calElement.tag
integrals[integral_type][cal_type] = dict()
for paramElement in calElement:
# <value>
valueElement = paramElement.find("value")
value = float(valueElement.text)
# <error>
errorElement = paramElement.find("error")
error = float(errorElement.text)
coeff = ufloat(value, error)
integrals[integral_type][cal_type][paramElement.tag] = coeff
if not integrals:
integrals = None
for integral_type in ['sub', 'bg']:
if integrals and not integral_type in integrals:
integrals[integral_type] = None
fit.integral = integrals
return (fit, success)