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|
#/*##########################################################################
#
# The PyMca X-Ray Fluorescence Toolkit
#
# Copyright (c) 2004-2019 European Synchrotron Radiation Facility
#
# This file is part of the PyMca X-ray Fluorescence Toolkit developed at
# the ESRF by the Software group.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
#############################################################################*/
__author__ = "V. Armando Sole - ESRF Data Analysis"
__contact__ = "sole@esrf.fr"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
import os
import sys
import time
MATPLOTLIB = True
from PyMca5.PyMcaGui import PyMcaQt as qt
QTVERSION = qt.qVersion()
#this is installation dependent I guess
from matplotlib import rcParams
from matplotlib import __version__ as matplotlib_version
#rcParams['numerix'] = "numeric"
from matplotlib.font_manager import FontProperties
from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas
from matplotlib.figure import Figure
MATPLOTLIB = True
from PyMca5.PyMcaIO import ConfigDict
from PyMca5.PyMcaCore import PyMcaLogo
from PyMca5.PyMcaPhysics.xrf import ConcentrationsTool
ConcentrationsConversion = ConcentrationsTool.ConcentrationsConversion
class QtMcaAdvancedFitReport:
def __init__(self, fitfile = None, outfile = None, outdir = None,
sourcename = None,
selection = None,
fitresult = None,htmltext=None,
concentrations=None, table = None,
plotdict=None):
self.concentrations = concentrations
self.concentrationsConversion = ConcentrationsConversion()
if table is None: table = 2
self.tableFlag = table
if fitfile is not None:
#generate output from fit result file
self.fitfile = fitfile
self.outfile = outfile
self.outdir = outdir
self.generateReportFromFitFile()
else:
#generate output from fitresult INCLUDING fit file
self.fitfile = fitfile
self.outfile = outfile
self.outdir = outdir
self.sourcename=sourcename
self.selection =selection
self.fitresult =fitresult
if self.outfile is None:
if selection is not None:
self.outfile = selection
if (self.outfile is None) or (self.outfile == 'Unknown Origin'):
if sourcename is not None:
self.outfile = os.path.basename(sourcename)
self.outfile = self.outfile.replace(" ","_")
self.outfile = self.outfile.replace("/","_over_")
self.graph = None
if htmltext is None:
htmltext={}
self.otherhtmltext=htmltext
if plotdict is None:
self.plotDict = {'logy':None,
'xmin':None,
'xmax':None,
'ymin':None,
'ymax':None}
else:
self.plotDict = plotdict
def writeReport(self,text=None):
if len(self.outfile) > 5:
if self.outfile[-5:] != ".html":
outfile = os.path.join(self.outdir, self.outfile+".html")
else:
outfile = os.path.join(self.outdir, self.outfile)
else:
outfile = os.path.join(self.outdir, self.outfile+".html")
try:
os.remove(outfile)
except:
pass
concentrationsfile = outfile[:-5]+"_concentrations.txt"
try:
os.remove(concentrationsfile)
except:
pass
if text is None:
text = self.getText()
f=open(outfile,"w")
f.write(text)
f.close()
if len(self._concentrationsTextASCII) > 1:
f=open(concentrationsfile, "w")
f.write(self._concentrationsTextASCII)
f.close()
return outfile
def generateReportFromFitFile(self):
d=ConfigDict.ConfigDict()
d.read(self.fitfile)
sourcename = "Unknown Source"
selection = "Unknown Selection"
if 'info' in d:
if 'key' in d['info']:
selection=d['info']['key']
elif 'Key' in d['info']:
selection=d['info']['Key']
for key in d['info'].keys():
if key.upper() == 'SOURCENAME':
sourcename = d['info'][key]
elif (key.upper() == 'SELECTION') or\
(key.upper() == 'LEGEND'):
selection = d['info'][key]
self.sourcename = sourcename
self.selection = selection
if self.outfile is None:
if self.outdir is None:
self.outdir = os.getcwd()
self.outfile= os.path.basename(self.fitfile)
else:
if self.outdir is None:
self.outdir = os.path.dirname(self.outfile)
self.outfile= os.path.basename(self.outfile)
if self.outdir == '':self.outdir = "."
self.fitresult=d
if 'concentrations' in d:
self.concentrations = d['concentrations']
def getText(self):
newlinks = []
for key in self.otherhtmltext.keys():
newlinks.append(["#%s" % (key),"%s" % key])
text =self.getHeader(newlinks)
text+=self.getInfo()
text+=self.getImage()
text+=self.getParam()
text+=self.getConcentrations()
self._concentrationsTextASCII = self.getConcentrationsASCII()
text+=self.getResult()
for key in self.otherhtmltext.keys():
text+="\n"
text+= "<H2><a NAME=""%s""></a><FONT color=#009999>" % key
text+= "%s:" % key
text+= "</FONT></H2>"
text+= self.otherhtmltext[key]
text+="<br>"
text+=self.getFooter()
return text
def getHeader(self,addlink=None):
link = [ ['http://pymca.sourceforge.net', 'PyMCA home'],
['http://www.esrf.fr', 'ESRF home'],
['http://www.esrf.fr/UsersAndScience/Experiments/TBS/BLISS', 'BLISS home']]
if self.concentrations is not None:
link.append(['#Concentrations', 'Concentrations'])
if self.tableFlag:link.append(['#Fit_Peak_Results', 'Fit Peak Results'])
if addlink is not None:
for item in addlink:
link.append(item)
text =""
text+= "<HTML>"
text+= "<HEAD>"
text+= "<TITLE>PyMCA : Advanced Fit Results</TITLE>"
text+= "</HEAD>"
text+= "<BODY TEXT=#000000 BGCOLOR=#FFFFFF ALINK=#ff6600 LINK=#0000cc VLINK=#0000cc marginwidth=10 marginheight=10 topmargin=10 leftmargin=10>"
text+= "<CENTER>"
text+= "<TABLE WIDTH=100%% border=0 Height=70>"
text+= " <TR>"
text+= " <TD><Font Size=5 Color=#0000cc>"
text+= " <b>PyMCA : Advanced Fit Results</b></Font>"
text+= " </td>"
text+= " <td rowspan=2 ALIGN=RIGHT VALIGN=bottom>"
text+= " <a HREF=""http://www.esrf.fr/"">"
logofile = self.outdir + "/" + "PyMcaLogo.png"
if not os.path.exists(logofile):
pixmap = qt.QPixmap(PyMcaLogo.PyMcaLogo)
pixmap.save(logofile,"PNG")
text+= " <img SRC=%s ALT=""ESRF home"" WIDTH=55 HEIGHT=68 BORDER=0></a>" % "PyMcaLogo.png"
text+= " </td>"
text+= " </tr>"
text+= " <tr>"
text+= " <td width=100%% VALIGN=bottom>"
text+= " <TABLE BORDER=0 CELLPADDING=0 CELLSPACING=0 WIDTH=100%%>"
text+= " <TR>"
text+= " <TD WIDTH=100%% BGCOLOR=#ee22aa HEIGHT=17 ALIGN=LEFT VALIGN=middle>"
text+= " <FONT color=#000000> "
for name in link:
text+= "| <A STYLE=""color: #FFFFFF"" HREF=""%s"">%s</a> "%(tuple(name))
text+= " </FONT>"
text+= " </TD>"
text+= " </TR>"
text+= " </TABLE>"
text+= " </td>"
text+= " </tr>"
text+= " <tr>"
text+= " <td colspan=2 height=5><spacer type=block height=10 width=0>"
text+= " </td>"
text+= " </tr>"
text+= "</table>"
text+= "</center>"
return text
def getInfo(self):
text =""
text+= "<nobr><H2><FONT color=#0000cc>"
text+= "Computed File : "
text+= "</FONT>"
text+= "<FONT color=#000000>"
if self.fitfile is not None:
if os.path.basename(self.fitfile) == self.fitfile:
text+= "<b><I>%s</I></b>" % (os.getcwd()+"/"+self.fitfile)
else:
text+= "<b><I>%s</I></b>" % (self.fitfile)
else:
text+= "<b><I>%s</I></b>" % (self.outdir+"/"+self.outfile+".fit")
#and I have to generate it!!!!!!!!!!!!"
d=ConfigDict.ConfigDict(self.fitresult)
try:
os.remove(self.outdir+"/"+self.outfile+".fit")
except:
pass
if self.concentrations is not None:
d['concentrations'] = self.concentrations
d.write(self.outdir+"/"+self.outfile+".fit")
text+= "</FONT>"
text+= "</H2>"
text+= "</nobr>"
text+= "<LEFT>"
text+= "<TABLE border=0>"
text+= "<TR><TD><SPACER TYPE=BLOCK WIDTH=50></TD><TD>"
text+= "<TABLE border=0 cellpadding=1 cellspacing=2>"
text+= " <TR><TH ALIGN=LEFT>Source : </TH><TD ALIGN=LEFT>%s</TD></TR>" % (self.sourcename)
text+= " <TR><TH ALIGN=LEFT>Selection : </TH><TD ALIGN=LEFT>%s</TD></TR>" % (self.selection)
text+= " <TR><TH ALIGN=LEFT>Parameters : </TH><TD ALIGN=LEFT>"
d=ConfigDict.ConfigDict(self.fitresult['result']['config'])
try:
os.remove(self.outdir+"/"+self.outfile+".txt")
except:
pass
d.write(self.outdir+"/"+self.outfile+".txt")
text+= "<a HREF=""%s"">%s</a>"% (self.outfile+".txt",self.outfile+".txt")
text+="</TD></TR>"
"""
text+= " <TR><TH ALIGN=RIGHT>Source : </TH><TD ALIGN=LEFT>%s</TD>"%(self.sourcename)
text+= " <TH ALIGN=RIGHT>Selection : </TH><TD ALIGN=LEFT>%s</TD></TR>"%(self.selection)
keys= [ key for key in info.keys() if key not in ['paramfile', 'peakfile'] ]
for idx in range(0, len(keys), 2):
text+= " <TR><TH ALIGN=RIGHT>%s : </TH><TD ALIGN=LEFT>%s</TD>"%(keys[idx], info[keys[idx]])
if idx+1<len(keys):
text+= " <TH ALIGN=RIGHT>%s : </TH><TD ALIGN=LEFT>%s</TD></TR>"%(keys[idx+1], info[keys[idx+1]])
else:
text+= " <TD COLSPAN=2></TD></TR>"
"""
text+= "</TABLE>"
text+= "</TD></TR></TABLE>"
text+= "</LEFT>"
return text
def getParam(self):
text=""
zero = self.fitresult['result']['fittedpar'][self.fitresult['result']['parameters'].index('Zero')]
gain = self.fitresult['result']['fittedpar'][self.fitresult['result']['parameters'].index('Gain')]
noise= self.fitresult['result']['fittedpar'][self.fitresult['result']['parameters'].index('Noise')]
fano = self.fitresult['result']['fittedpar'][self.fitresult['result']['parameters'].index('Fano')]
sum = self.fitresult['result']['fittedpar'][self.fitresult['result']['parameters'].index('Sum')]
stdzero = self.fitresult['result']['sigmapar'][self.fitresult['result']['parameters'].index('Zero')]
stdgain = self.fitresult['result']['sigmapar'][self.fitresult['result']['parameters'].index('Gain')]
stdnoise= self.fitresult['result']['sigmapar'][self.fitresult['result']['parameters'].index('Noise')]
stdfano = self.fitresult['result']['sigmapar'][self.fitresult['result']['parameters'].index('Fano')]
stdsum = self.fitresult['result']['sigmapar'][self.fitresult['result']['parameters'].index('Sum')]
hypermetflag = self.fitresult['result']['config']['fit']['hypermetflag']
if not ('fitfunction' in self.fitresult['result']['config']['fit']):
if hypermetflag:
self.fitresult['result']['config']['fit']['fitfunction'] = 0
else:
self.fitresult['result']['config']['fit']['fitfunction'] = 1
if self.fitresult['result']['config']['fit']['fitfunction'] or\
(hypermetflag != 1):
#the peaks are not pure gaussians
if self.fitresult['result']['config']['fit']['fitfunction']:
#peaks are pseudo-voigt functions
hypermetnames = ['Eta Factor']
else:
hypermetnames = ['ST AreaR', 'ST SlopeR',
'LT AreaR', 'LT SlopeR',
'STEP HeightR']
hypermetvalues=[]
hypermetstd =[]
hypermetfinalnames = []
for name in hypermetnames:
if name in self.fitresult['result']['parameters']:
hypermetvalues.append(self.fitresult['result']['fittedpar'] \
[self.fitresult['result']['parameters'].index(name)])
hypermetstd.append(self.fitresult['result']['sigmapar'] \
[self.fitresult['result']['parameters'].index(name)])
hypermetfinalnames.append(name)
# --- html table
text+="<H2><FONT color=#009999>"
text+="Fit Parameters :"
text+="</FONT></H2>"
text+="<CENTER>"
text+="<TABLE border=0 cellpadding=0 cellspacing=2 width=80%>"
text+="<TR>"
text+=" <TD><TABLE border=1 cellpadding=1 cellspacing=0 width=100%>"
text+=" <TR align=center>"
text+=" <TH colspan=2>FIT parameters</TH>"
text+=" </TR>"
text+=" <TR align=left>"
text+=" <TD><I> Region of Fit</I></TD>"
text+=" <TD> %d - %d</TD>" % (self.fitresult['result']['config']['fit']['xmin'],self.fitresult['result']['config']['fit']['xmax'])
text+=" </TR>"
text+=" <TR align=left>"
text+=" <TD><I> Number of iterations</I></TD>"
#text+=" <TD> %d</TD>" % (fitpar['fit_numiter'])
text+=" <TD> %d</TD>" % (self.fitresult['result']['niter'])
text+=" </TR>"
text+=" <TR align=left>"
text+=" <TD><I> Chi square</I></TD>"
#text+=" <TD> %.4f</TD>" % (fitpar['fit_chi'])
text+=" <TD> %.4f</TD>" % (self.fitresult['result']['chisq'])
text+=" </TR>"
text+=" <TR align=left>"
text+=" <TD><I> Last Chi square difference</I></TD>"
#text+=" <TD> %.4f %%</TD>" % (fitpar['fit_lastchi'])
text+=" <TD> %.4f %%</TD>" % (self.fitresult['result']['lastdeltachi']*100)
text+=" </TR>"
text+=" </TABLE>"
text+=" </TD>"
text+="</TR>"
text+="<TR>"
text+=" <TD><TABLE border=1 cellpadding=1 cellspacing=0 width=100%>"
text+=" <TR align=center>"
text+=" <TH colspan=2>Calibration parameters</TH>"
text+=" </TR>"
text+=" <TR align=left>"
text+=" <TD><I> Zero</I></TD>"
text+=" <TD> % .5E +/- % .5E</TD>" % (zero, stdzero)
text+=" </TR>"
text+=" <TR align=left>"
text+=" <TD><I> Gain</I></TD>"
text+=" <TD> % .5E +/- % .5E</TD>" % (gain, stdgain)
text+=" </TR>"
text+=" <TR align=left>"
text+=" <TD><I> Noise</I></TD>"
text+=" <TD> % .5E +/- % .5E</TD>" % (noise, stdnoise)
text+=" </TR>"
text+=" <TR align=left>"
text+=" <TD><I> Fano</I></TD>"
text+=" <TD> % .5E +/- % .5E</TD>" % (fano, stdfano)
text+=" </TR>"
text+=" <TR align=left>"
text+=" <TD><I> Sum</I></TD>"
text+=" <TD> % .5E +/- % .5E</TD>" % (sum, stdsum)
text+=" </TR>"
text+=" </TABLE>"
text+=" </TD>"
text+="</TR>"
# --- Peak shape parameters ---
if hypermetflag != 1:
text+="<TR>"
text+=" <TD><TABLE border=1 cellpadding=1 cellspacing=0 width=100%>"
text+=" <TR align=center>"
text+=" <TH colspan=2>Peak shape parameters</TH>"
text+=" </TR>"
for i in range(len(hypermetfinalnames)):
text+=" <TR align=left>"
text+=" <TD><I> %s</I></TD>" % hypermetnames[i]
text+=" <TD> % .5E +/- % .5E</TD>" % (hypermetvalues[i],
hypermetstd[i])
text+=" </TR>"
text+=" </TABLE>"
text+=" </TD>"
text+="</TR>"
# --- Continuum parameters ---
text+="<TR>"
text+=" <TD><TABLE border=1 cellpadding=1 cellspacing=0 width=100%>"
text+=" <TR align=center>"
text+=" <TH colspan=2>Continuum parameters</TH>"
text+=" </TR>"
# Stripping
if self.fitresult['result']['config']['fit']['stripflag']:
constant = 1.0
iterations = 20000
stripwidth = 1
stripfilterwidth = 1
stripalgorithm = 0
snipwidth = 30
if 'stripalgorithm' in self.fitresult['result']['config']['fit']:
stripalgorithm=self.fitresult['result']['config']['fit']['stripalgorithm']
if 'snipwidth' in self.fitresult['result']['config']['fit']:
snipwidth=self.fitresult['result']['config']['fit']['snipwidth']
if 'stripconstant' in self.fitresult['result']['config']['fit']:
constant=self.fitresult['result']['config']['fit']['stripconstant']
if 'stripiterations' in self.fitresult['result']['config']['fit']:
iterations=self.fitresult['result']['config']['fit']['stripiterations']
if 'stripwidth' in self.fitresult['result']['config']['fit']:
stripwidth=self.fitresult['result']['config']['fit']['stripwidth']
if 'stripfilterwidth' in self.fitresult['result']['config']['fit']:
stripfilterwidth=self.fitresult['result']['config']['fit']['stripfilterwidth']
if stripalgorithm == 1:
text+=" <TR align=left>"
text+=" <TD><I> Type</I></TD>"
text+=" <TD> %s</TD>" % "SNIP Background"
text+=" </TR>"
text+=" <TR align=left>"
text+=" <TD><I> %s<I></TD>" % "SNIP width"
text+=" <TD> %.5f</TD>" % snipwidth
text+=" </TR>"
else:
text+=" <TR align=left>"
text+=" <TD><I> Type</I></TD>"
text+=" <TD> %s</TD>" % "Strip Background"
text+=" </TR>"
text+=" <TR align=left>"
text+=" <TD><I> %s<I></TD>" % "Strip Constant"
text+=" <TD> %.5f</TD>" % constant
text+=" </TR>"
text+=" <TR align=left>"
text+=" <TD><I> %s<I></TD>" % "Strip Iterations"
text+=" <TD> %d</TD>" % iterations
text+=" </TR>"
text+=" <TR align=left>"
text+=" <TD><I> %s<I></TD>" % "Strip Width"
text+=" <TD> %d</TD>" % stripwidth
text+=" </TR>"
text+=" <TR align=left>"
text+=" <TD><I> %s<I></TD>" % "Smoothing Filter Width"
text+=" <TD> %d</TD>" % stripfilterwidth
text+=" </TR>"
stripanchorslist = []
stripanchorsflag = self.fitresult['result']['config']['fit'].get('stripanchorsflag', 0)
if stripanchorsflag:
stripanchorslist = self.fitresult['result']['config']['fit'].get('stripanchorslist', [])
i = 0
for anchor in stripanchorslist:
if anchor != 0:
text+=" <TR align=left>"
text+=" <TD><I> %s%d<I></TD>" % ("Anchor",i)
text+=" <TD> %d</TD>" % anchor
text+=" </TR>"
i += 1
# --- Background Function
if self.fitresult['result']['config']['fit']['continuum']:
text+=" <TR align=left>"
text+=" <TD><I> Type</I></TD>"
if 'continuum_name' in self.fitresult['result']['config']['fit']:
name = self.fitresult['result']['config']['fit']['continuum_name']
text+=" <TD> %s</TD>" % name
elif self.fitresult['result']['config']['fit']['continuum'] == 1:
text+=" <TD> %s</TD>" % "Constant Polymomial"
elif self.fitresult['result']['config']['fit']['continuum'] == 2:
text+=" <TD> %s</TD>" % "1st Order Polymomial"
elif self.fitresult['result']['config']['fit']['continuum'] == 3:
text+=" <TD> %s</TD>" % "2nd Order Polymomial"
else:
#compatibility with previous versions
text+=" <TD> %s</TD>" % "1st Order Polymomial"
text+=" </TR>"
isum = self.fitresult['result']['parameters'].index('Sum')
a=0
if hypermetflag:a=5
nglobal = len(self.fitresult['result']['parameters']) - len(self.fitresult['result']['groups'])
for i in range(isum+1,nglobal-a):
text+=" <TR align=left>"
text+=" <TD><I> %s<I></TD>" % self.fitresult['result']['parameters'][i]
value = self.fitresult['result']['fittedpar'][i]
stdvalue = self.fitresult['result']['sigmapar'] [i]
text+=" <TD> % .5E +/- % .5E</TD>" % (value, stdvalue)
text+=" </TR>"
if 0:
text+=" <TR align=left>"
text+=" <TD><I> %s<I></TD>" % 'Constant'
value = self.fitresult['result']['fittedpar'][self.fitresult['result']['parameters'].index('Constant')]
stdvalue = self.fitresult['result']['sigmapar'] [self.fitresult['result']['parameters'].index('Constant')]
text+=" <TD> % .5E +/- % .5E</TD>" % (value, stdvalue)
text+=" </TR>"
if self.fitresult['result']['config']['fit']['continuum'] > 1:
text+=" <TR align=left>"
text+=" <TD><I> %s<I></TD>" % 'Slope'
value = self.fitresult['result']['fittedpar'][self.fitresult['result']['parameters'].index('Constant')+1]
stdvalue = self.fitresult['result']['sigmapar'] [self.fitresult['result']['parameters'].index('Constant')+1]
text+=" <TD> % .5E +/- % .5E</TD>" % (value, stdvalue)
text+=" </TR>"
text+="</TR>"
text+=" </TABLE>"
text+=" </TD>"
text+="</TR>"
if 0:
#not yet implemented
text+="<TR>"
text+=" <TD align=center>"
text+=" <I>FIT END STATUS : </I>%s<BR>"% "STATUS"
text+=" <B>%s</B>" % "MESSAGE"
text+=" </TD>"
text+="</TR>"
text+="</TABLE>"
text+="</CENTER>"
return text
def getFooter(self):
now = time.time()
text =""
text+= "<center>"
text+= "<table width=100%% border=0 cellspacing=0 cellpadding=0>"
text+= " <tr><td colspan=2 height=10><spacer type=block height=10 width=0></td></tr>"
text+= " <tr><td colspan=2 bgcolor=#cc0066 height=5><spacer type=block height=5 width=0></td></tr>"
text+= " <tr><td colspan=2 height=5><spacer type=block height=5 width=0></td></tr>"
text+= " <TR>"
text+= " <TD><FONT size=1 >created: %s</font></TD>" % time.ctime(now)
#text+= " <TD ALIGN=RIGHT><FONT size=1 >last modified: %s" % time.ctime(now)
text+= " <TD ALIGN=RIGHT><FONT size=1 >last modified: %s by" % time.ctime(now)
#text+= " <A STYLE=""color: #0000cc"" HREF=""mailto:papillon@esrf.fr"">papillon@esrf.fr</A></FONT></TD>"
if sys.platform == 'win32':
try:
user = os.getenv('USERNAME')
text+= " <A STYLE=""color: #0000cc"">%s</A></FONT></TD>" % user
except:
text +="</FONT></TD>"
else:
try:
user = os.getenv("USER")
text+= " <A STYLE=""color: #0000cc"">%s</A></FONT></TD>" % user
except:
text +="</FONT></TD>"
text+= " </TR>"
text+= "</TABLE>"
text+= "</center>"
text+= "</BODY>"
text+= "</HTML>"
return text
def __getFitImage(self,imagefile=None):
if imagefile is None:imagefile=self.outdir+"/"+self.outfile+".png"
filelink = "%s" % imagefile
text = ""
text+= "<H2><FONT color=#009999>"
text+= "Spectrum, Continuum and Fitted values :"
text+= "</FONT></H2>"
text+= "<CENTER>"
text+= "<IMG SRC=%s ALT=""fit graph"" ALIGN=center>"%filelink
text+= "</CENTER>"
return text
def getImage(self):
ddict=self.fitresult
try:
fig = Figure(figsize=(6,3)) # in inches
canvas = FigureCanvas(fig)
ax = fig.add_axes([.15, .15, .8, .8])
ax.set_axisbelow(True)
logplot = self.plotDict.get('logy', True)
if logplot is None:
if (ddict['result']['ydata'].max() - ddict['result']['ydata'].min()) < 200:
logplot = False
elif ddict['result']['yfit'].min() < 0.01:
logplot = False
else:
logplot = True
if logplot:
axplot = ax.semilogy
else:
axplot = ax.plot
axplot(ddict['result']['energy'], ddict['result']['ydata'], 'k', lw=1.5)
axplot(ddict['result']['energy'], ddict['result']['continuum'], 'g', lw=1.5)
legendlist = ['spectrum', 'continuum', 'fit']
axplot(ddict['result']['energy'], ddict['result']['yfit'], 'r', lw=1.5)
fontproperties = FontProperties(size=8)
if ddict['result']['config']['fit']['sumflag']:
axplot(ddict['result']['energy'],
ddict['result']['pileup'] + ddict['result']['continuum'], 'y', lw=1.5)
legendlist.append('pileup')
if matplotlib_version < '0.99.0':
legend = ax.legend(legendlist,0,
prop = fontproperties, labelsep=0.02)
elif matplotlib_version < '1.5':
legend = ax.legend(legendlist,0,
prop = fontproperties, labelspacing=0.02)
else:
legend = ax.legend(legendlist, loc=0,
prop = fontproperties, labelspacing=0.02)
except ValueError:
# It seems this error is not caught with matplotlib 2.2.4 and the
# report crashes instead of switching to a linear plot
fig = Figure(figsize=(6,3)) # in inches
canvas = FigureCanvas(fig)
ax = fig.add_axes([.15, .15, .8, .8])
ax.set_axisbelow(True)
ax.plot(ddict['result']['energy'], ddict['result']['ydata'], 'k', lw=1.5)
ax.plot(ddict['result']['energy'], ddict['result']['continuum'], 'g', lw=1.5)
legendlist = ['spectrum', 'continuum', 'fit']
ax.plot(ddict['result']['energy'], ddict['result']['yfit'], 'r', lw=1.5)
fontproperties = FontProperties(size=8)
if ddict['result']['config']['fit']['sumflag']:
ax.plot(ddict['result']['energy'],
ddict['result']['pileup'] + ddict['result']['continuum'], 'y', lw=1.5)
legendlist.append('pileup')
if matplotlib_version < '0.99.0':
legend = ax.legend(legendlist,0,
prop = fontproperties, labelsep=0.02)
elif matplotlib_version < '1.5':
legend = ax.legend(legendlist,0,
prop = fontproperties, labelspacing=0.02)
else:
legend = ax.legend(legendlist, loc=0,
prop = fontproperties, labelspacing=0.02)
ax.set_xlabel('Energy')
ax.set_ylabel('Counts')
legend.draw_frame(False)
outfile = self.outdir+"/"+self.outfile+".png"
try:
os.remove(outfile)
except:
pass
canvas.print_figure(outfile)
return self.__getFitImage(self.outfile+".png")
def getConcentrations(self):
return self.concentrationsConversion.getConcentrationsAsHtml(\
self.concentrations)
def getConcentrationsASCII(self):
return self.concentrationsConversion.getConcentrationsAsAscii(\
self.concentrations)
def getResult(self):
text = ""
if self.tableFlag == 0:
return text
text+="\n"
text+= "<H2><a NAME=""%s""></a><FONT color=#009999>" % 'Fit_Peak_Results'
text+= "%s:" % 'Fit Peak Results'
text+= "</FONT></H2>"
text+="<br>"
result = self.fitresult['result']
if self.tableFlag == 1:
labels=['Element','Group','Fit Area','Sigma']
else:
labels=['Element','Group','Fit Area','Sigma','Energy','Ratio','FWHM','Chi square']
lemmon = ("#%x%x%x" % (255,250,205)).upper()
hcolor = ("#%x%x%x" % (230,240,249)).upper()
text += "<CENTER>"
text += ("<nobr>")
text += '<table width="80%" border="0" cellspacing="1" cellpadding="1" >'
text += ( "<tr><b>")
for l in range(len(labels)):
if l < 2:
text += '<td align="left" bgcolor=%s><b>%s</b></td>' % (hcolor,labels[l])
elif (l > 3) or (self.tableFlag == 1):
text += '<td align="right" bgcolor=%s><b>%s</b></td>' % (hcolor,labels[l])
else:
text += '<td align="center" bgcolor=%s><b>%s</b></td>' % (hcolor,labels[l])
text+="</b></tr>\n"
for group in result['groups']:
text+=("<tr>")
ele,group0 = group.split()
text += '<td align="left"><b>%s</b></td>' % ele
text += '<td align="left"><b>%s</b></td>' % group0
fitarea = "%.6e" % result[group]['fitarea']
sigmaarea = "%.2e" % result[group]['sigmaarea']
text += '<td align="right"><b>%s</b></td>' % fitarea
text += '<td align="right"><b>%s</b></td>' % sigmaarea
text += '<td align="right"><b> </b></td>'
text += '<td align="right"><b> </b></td>'
text += '<td align="right"><b> </b></td>'
text += '<td align="right"><b> </b></td>'
text += '</tr>\n'
if type(result[group]['peaks']) != type([]):
iterator = [result[group]['peaks']]
else:
iterator = 1 * result[group]['peaks']
if self.tableFlag == 1:
iterator = []
for peak in iterator:
text += '<tr><td> </td>'
name = peak
energy = ("%.3f" % (result[group][peak]['energy']))
ratio = ("%.5f" % (result[group][peak]['ratio']))
area = ("%.6e" % (result[group][peak]['fitarea']))
sigma = ("%.2e" % (result[group][peak]['sigmaarea']))
fwhm = ("%.3f" % (result[group][peak]['fwhm']))
chisq = ("%.2f" % (result[group][peak]['chisq']))
fields = [name,area,sigma,energy,ratio,fwhm,chisq]
for field in fields:
if field == name:
text+=('<td align="left" bgcolor=%s>%s</td>' % (lemmon,field))
else:
text+=('<td align="right" bgcolor=%s>%s</td>' % (lemmon,field))
text+="</tr>\n"
if type(result[group]['escapepeaks']) != type([]):
iterator = [result[group]['escapepeaks']]
else:
iterator = 1 * result[group]['escapepeaks']
if self.tableFlag == 1:
iterator = []
for peak0 in iterator:
name = peak0+"esc"
peak = peak0+"esc"
if result[group][name]['ratio'] > 0.0:
text += '<tr><td></td>'
energy = ("%.3f" % (result[group][peak]['energy']))
ratio = ("%.5f" % (result[group][peak]['ratio']))
area = ("%.6e" % (result[group][peak]['fitarea']))
sigma = ("%.2e" % (result[group][peak]['sigmaarea']))
fwhm = ("%.3f" % (result[group][peak]['fwhm']))
chisq = ("%.2f" % (result[group][peak]['chisq']))
fields = [name,area,sigma,energy,ratio,fwhm,chisq]
for field in fields:
if field == name:
text+=('<td align="left" bgcolor=%s>%s</td>' % (lemmon,field))
else:
text+=('<td align="right" bgcolor=%s>%s</td>' % (lemmon,field))
text+="</tr>\n"
text+=("</table>")
text+=("</nobr>")
text+="</CENTER>"
return text
def generateoutput(fitfile,outfile=None):
report = QtMcaAdvancedFitReport(fitfile, outfile)
report.writeReport()
if __name__ == "__main__":
if len(sys.argv) <2 :
print("Usage: %s Input_Fit_Result_File [optional_output_file]" %\
sys.argv[0])
sys.exit(1)
app = qt.QApplication(sys.argv)
fitfile=sys.argv[1]
if len(sys.argv) > 2:
outfile = sys.argv[2]
else:
outfile = None
generateoutput(fitfile,outfile)
app.quit()
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