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McaAdvancedFit.py
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McaAdvancedFit.py
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#/*##########################################################################
#
# The PyMca X-Ray Fluorescence Toolkit
#
# Copyright (c) 2004-2023 European Synchrotron Radiation Facility
#
# This file is part of the PyMca X-ray Fluorescence Toolkit developed at
# the ESRF.
#
# 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"
__contact__ = "sole@esrf.fr"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
import sys
import os
import numpy
import time
import copy
import logging
import tempfile
import shutil
import traceback
from PyMca5.PyMcaGui import PyMcaQt as qt
if hasattr(qt, "QString"):
QString = qt.QString
else:
QString = qt.safe_str
QTVERSION = qt.qVersion()
from PyMca5.PyMcaGui.pymca import QPyMcaMatplotlibSave1D
MATPLOTLIB = True
#force understanding of utf-8 encoding
#otherways it cannot generate svg output
try:
import encodings.utf_8
except Exception:
#not a big problem
pass
from PyMca5.PyMcaPhysics.xrf import ClassMcaTheory
FISX = ClassMcaTheory.FISX
if FISX:
FisxHelper = ClassMcaTheory.FisxHelper
from PyMca5.PyMcaGui.physics.xrf import FitParam
from PyMca5.PyMcaGui.physics.xrf import McaAdvancedTable
from PyMca5.PyMcaGui.physics.xrf import QtMcaAdvancedFitReport
from PyMca5.PyMcaGui.physics.xrf import ConcentrationsWidget
from PyMca5.PyMcaPhysics.xrf import ConcentrationsTool
from PyMca5.PyMcaGui.plotting import PlotWindow
from PyMca5.PyMcaGui.plotting import PyMca_Icons
IconDict = PyMca_Icons.IconDict
from PyMca5.PyMcaGui.physics.xrf import McaCalWidget
from PyMca5.PyMcaGui.physics.xrf import PeakIdentifier
from PyMca5.PyMcaGui.misc import SubprocessLogWidget
from PyMca5.PyMcaGui.physics.xrf import ElementsInfo
Elements = ElementsInfo.Elements
#import McaROIWidget
from PyMca5.PyMcaGui.plotting import PyMcaPrintPreview
from PyMca5.PyMcaCore import PyMcaDirs
from PyMca5.PyMcaIO import ConfigDict
from PyMca5.PyMcaGui.misc import CalculationThread
from PyMca5.PyMcaGui.io import PyMcaFileDialogs
_logger = logging.getLogger(__name__)
_logger.debug("############################################\n"
"# McaAdvancedFit is in DEBUG mode #\n"
"############################################")
XRFMC_FLAG = False
try:
from PyMca5.PyMcaPhysics.xrf.XRFMC import XRFMCHelper
XRFMC_FLAG = True
except ImportError:
_logger.warning("Cannot import XRFMCHelper module")
if _logger.getEffectiveLevel() == logging.DEBUG:
raise
USE_BOLD_FONT = True
class McaAdvancedFit(qt.QWidget):
"""
This class inherits QWidget.
It provides all the functionality required to perform an interactive fit
and to generate a configuration file.
It is the simplest way to embed PyMca's fitting functionality into other
PyQt application.
It can be used from the interactive prompt of ipython provided ipython is
started with the -q4thread flag.
**Usage**
>>> from PyMca5 import McaAdvancedFit
>>> w = McaAdvancedFit.McaAdvancedFit()
>>> w.setData(x=x, y=y) # x is your channel array and y the counts array
>>> w.show()
"""
sigMcaAdvancedFitSignal = qt.pyqtSignal(object)
def __init__(self, parent=None, name="PyMca - McaAdvancedFit",fl=0,
sections=None, top=True, margin=11, spacing=6):
qt.QWidget.__init__(self, parent)
self.setWindowTitle(name)
self.setWindowIcon(qt.QIcon(qt.QPixmap(IconDict['gioconda16'])))
self.lastInputDir = None
self.configDialog = None
self.matplotlibDialog = None
self.mainLayout = qt.QVBoxLayout(self)
self.mainLayout.setContentsMargins(margin, margin, margin, margin)
self.mainLayout.setSpacing(0)
if sections is None:
sections=["TABLE"]
self.headerLabel = qt.QLabel(self)
self.mainLayout.addWidget(self.headerLabel)
self.headerLabel.setAlignment(qt.Qt.AlignHCenter)
font = self.font()
font.setBold(USE_BOLD_FONT)
self.headerLabel.setFont(font)
self.setHeader('Fit of XXXXXXXXXX from Channel XXXXX to XXXX')
self.top = Top(self)
self.mainLayout.addWidget(self.top)
self.sthread = None
self.elementsInfo = None
self.identifier = None
self.logWidget = None
if False and len(sections) == 1:
w = self
self.mcatable = McaAdvancedTable.McaTable(w)
self.concentrationsWidget = None
else:
self.mainTab = qt.QTabWidget(self)
self.mainLayout.addWidget(self.mainTab)
#graph
self.tabGraph = qt.QWidget()
tabGraphLayout = qt.QVBoxLayout(self.tabGraph)
tabGraphLayout.setContentsMargins(margin, margin, margin, margin)
tabGraphLayout.setSpacing(spacing)
#self.graphToolbar = qt.QHBox(self.tabGraph)
self.graphWindow = McaGraphWindow(self.tabGraph)
tabGraphLayout.addWidget(self.graphWindow)
self.graph = self.graphWindow
self.graph.setGraphXLabel('Channel')
self.graph.setGraphYLabel('Counts')
self.mainTab.addTab(self.tabGraph, "GRAPH")
self.graphWindow.sigPlotSignal.connect(self._mcaGraphSignalSlot)
#table
self.tabMca = qt.QWidget()
tabMcaLayout = qt.QVBoxLayout(self.tabMca)
tabMcaLayout.setContentsMargins(margin, margin, margin, margin)
tabMcaLayout.setSpacing(spacing)
w = self.tabMca
line = Line(w, info="TABLE")
tabMcaLayout.addWidget(line)
line.setToolTip("DoubleClick toggles floating window mode")
self.mcatable = McaAdvancedTable.McaTable(w)
tabMcaLayout.addWidget(self.mcatable)
self.mainTab.addTab(w,"TABLE")
line.sigLineDoubleClickEvent.connect(self._tabReparent)
self.mcatable.sigClosed.connect(self._mcatableClose)
#concentrations
self.tabConcentrations = qt.QWidget()
tabConcentrationsLayout = qt.QVBoxLayout(self.tabConcentrations)
tabConcentrationsLayout.setContentsMargins(margin,
margin,
margin,
margin)
tabConcentrationsLayout.setSpacing(0)
line2 = Line(self.tabConcentrations, info="CONCENTRATIONS")
self.concentrationsWidget = ConcentrationsWidget.Concentrations(self.tabConcentrations)
tabConcentrationsLayout.addWidget(line2)
tabConcentrationsLayout.addWidget(self.concentrationsWidget)
self.mainTab.addTab(self.tabConcentrations,"CONCENTRATIONS")
line2.setToolTip("DoubleClick toggles floating window mode")
self.concentrationsWidget.sigConcentrationsSignal.connect( \
self.__configureFromConcentrations)
line2.sigLineDoubleClickEvent.connect(self._tabReparent)
self.concentrationsWidget.sigClosed.connect( \
self._concentrationsWidgetClose)
#diagnostics
self.tabDiagnostics = qt.QWidget()
tabDiagnosticsLayout = qt.QVBoxLayout(self.tabDiagnostics)
tabDiagnosticsLayout.setContentsMargins(margin, margin, margin, margin)
tabDiagnosticsLayout.setSpacing(spacing)
w = self.tabDiagnostics
self.diagnosticsWidget = qt.QTextEdit(w)
self.diagnosticsWidget.setReadOnly(1)
tabDiagnosticsLayout.addWidget(self.diagnosticsWidget)
self.mainTab.addTab(w, "DIAGNOSTICS")
self.mainTab.currentChanged[int].connect(self._tabChanged)
self._energyAxis = False
self.__printmenu = qt.QMenu()
self.__printmenu.addAction(QString("Calibrate"), self._calibrate)
self.__printmenu.addAction(QString("Identify Peaks"),self.__peakIdentifier)
self.__printmenu.addAction(QString("Elements Info"), self.__elementsInfo)
self.outdir = None
self.configDir = None
self.__lastreport= None
self.browser = None
self.info = {}
self.__fitdone = 0
self._concentrationsDict = None
self._concentrationsInfo = None
self._xrfmcMatrixSpectra = None
#self.graph.hide()
#self.guiconfig = FitParam.Fitparam()
"""
self.specfitGUI.guiconfig.MCACheckBox.setEnabled(0)
palette = self.specfitGUI.guiconfig.MCACheckBox.palette()
palette.setDisabled(palette.active())
"""
##############
hbox=qt.QWidget(self)
self.bottom = hbox
hboxLayout = qt.QHBoxLayout(hbox)
hboxLayout.setContentsMargins(0, 0, 0, 0)
hboxLayout.setSpacing(4)
if not top:
self.configureButton = qt.QPushButton(hbox)
self.configureButton.setText("Configure")
self.toolsButton = qt.QPushButton(hbox)
self.toolsButton.setText("Tools")
hboxLayout.addWidget(self.configureButton)
hboxLayout.addWidget(self.toolsButton)
hboxLayout.addWidget(qt.HorizontalSpacer(hbox))
self.fitButton = qt.QPushButton(hbox)
hboxLayout.addWidget(self.fitButton)
#font = self.fitButton.font()
#font.setBold(True)
#self.fitButton.setFont(font)
self.fitButton.setText("Fit Again!")
self.printButton = qt.QPushButton(hbox)
hboxLayout.addWidget(self.printButton)
self.printButton.setText("Print")
self.htmlReportButton = qt.QPushButton(hbox)
hboxLayout.addWidget(self.htmlReportButton)
self.htmlReportButton.setText("HTML Report")
self.matrixSpectrumButton = qt.QPushButton(hbox)
hboxLayout.addWidget(self.matrixSpectrumButton)
self.matrixSpectrumButton.setText("Matrix Spectrum")
self.matrixXRFMCSpectrumButton = qt.QPushButton(hbox)
self.matrixXRFMCSpectrumButton.setText("MC Matrix Spectrum")
hboxLayout.addWidget(self.matrixXRFMCSpectrumButton)
self.matrixXRFMCSpectrumButton.hide()
self.peaksSpectrumButton = qt.QPushButton(hbox)
hboxLayout.addWidget(self.peaksSpectrumButton)
self.peaksSpectrumButton.setText("Peaks Spectrum")
self.matrixSpectrumButton.setCheckable(1)
self.peaksSpectrumButton.setCheckable(1)
hboxLayout.addWidget(qt.HorizontalSpacer(hbox))
self.dismissButton = qt.QPushButton(hbox)
hboxLayout.addWidget(self.dismissButton)
self.dismissButton.setText("Dismiss")
hboxLayout.addWidget(qt.HorizontalSpacer(hbox))
self.mainLayout.addWidget(hbox)
self.printButton.setToolTip('Print Active Tab')
self.htmlReportButton.setToolTip('Generate Browser Compatible Output\nin Chosen Directory')
self.matrixSpectrumButton.setToolTip('Toggle Matrix Spectrum Calculation On/Off')
self.matrixXRFMCSpectrumButton.setToolTip('Calculate Matrix Spectrum Using Monte Carlo')
self.peaksSpectrumButton.setToolTip('Toggle Individual Peaks Spectrum Calculation On/Off')
self.mcafit = ClassMcaTheory.McaTheory()
self.fitButton.clicked.connect(self.fit)
self.printButton.clicked.connect(self.printActiveTab)
self.htmlReportButton.clicked.connect(self.htmlReport)
self.matrixSpectrumButton.clicked.connect(self.__toggleMatrixSpectrum)
if self.matrixXRFMCSpectrumButton is not None:
self.matrixXRFMCSpectrumButton.clicked.connect(self.xrfmcSpectrum)
self.peaksSpectrumButton.clicked.connect(self.__togglePeaksSpectrum)
self.dismissButton.clicked.connect(self.dismiss)
self.top.configureButton.clicked.connect(self.__configure)
self.top.printButton.clicked.connect(self.__printps)
if top:
self.top.sigTopSignal.connect(self.__updatefromtop)
else:
self.top.hide()
self.configureButton.clicked.connect(self.__configure)
self.toolsButton.clicked.connect(self.__printps)
self._updateTop()
def __mainTabPatch(self, index):
return self.mainTabLabels[index]
def _fitdone(self):
if self.__fitdone:
return True
else:
return False
def refreshWidgets(self):
"""
This method just forces the graphical widgets to get updated.
It should be called if somehow you have modified the fit and/
or concentrations parameters by other means than the graphical
interface.
"""
self.__configure(justupdate=True)
def configure(self, ddict=None):
"""
This methods configures the fitting parameters and updates the
graphical interface.
It returns the current configuration.
"""
if ddict is None:
return self.mcafit.configure(ddict)
#configure and get the new configuration
newConfig = self.mcafit.configure(ddict)
#refresh the interface
self.refreshWidgets()
#return the current configuration
return newConfig
def __configure(self, justupdate=False):
config = {}
config.update(self.mcafit.config)
#config['fit']['use_limit'] = 1
if not justupdate:
if self.configDialog is None:
if self.__fitdone:
dialog = FitParam.FitParamDialog(modal=1,
fl=0,
initdir=self.configDir,
fitresult=self.dict['result'])
else:
dialog = FitParam.FitParamDialog(modal=1,
fl=0,
initdir=self.configDir,
fitresult=None)
dialog.fitparam.peakTable.sigFitPeakSelect.connect( \
self.__elementclicked)
self.configDialog = dialog
else:
dialog = self.configDialog
if self.__fitdone:
dialog.setFitResult(self.dict['result'])
else:
dialog.setFitResult(None)
if self.__fitdone:
# a direct fit without loading the file can lead to errors
lastTime = self.mcafit.getLastTime()
self.info["time"] = lastTime
dialog.setParameters(self.mcafit.getStartingConfiguration())
dialog.setData(self.mcafit.xdata * 1.0,
self.mcafit.ydata * 1.0,
info=copy.deepcopy(self.info))
#dialog.fitparam.regionCheck.setDisabled(True)
#dialog.fitparam.minSpin.setDisabled(True)
#dialog.fitparam.maxSpin.setDisabled(True)
ret = dialog.exec()
if dialog.initDir is not None:
self.configDir = 1 * dialog.initDir
else:
self.configDir = None
if ret != qt.QDialog.Accepted:
dialog.close()
#del dialog
return
try:
#this may crash in qt 2.3.0
npar = dialog.getParameters()
except Exception:
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Error occured getting parameters:")
msg.setInformativeText(str(sys.exc_info()[1]))
msg.setDetailedText(traceback.format_exc())
msg.exec()
return
config.update(npar)
dialog.close()
#del dialog
self.graph.clearMarkers()
self.graph.replot()
self.__fitdone = False
self._concentrationsDict = None
self._concentrationsInfo = None
self._xrfmcMatrixSpectra = None
if self.concentrationsWidget is not None:
self.concentrationsWidget.concentrationsTable.setRowCount(0)
if self.mcatable is not None:
self.mcatable.setRowCount(0)
self.diagnosticsWidget.clear()
#make sure newly or redefined materials are added to the
#materials in the fit configuration
for material in Elements.Material.keys():
self.mcafit.config['materials'][material] =copy.deepcopy(Elements.Material[material])
hideButton = True
if 'xrfmc' in config:
programFile = config['xrfmc'].get('program', None)
if programFile is not None:
if os.path.exists(programFile):
if os.path.isfile(config['xrfmc']['program']):
hideButton = False
if hideButton:
self.matrixXRFMCSpectrumButton.hide()
else:
self.matrixXRFMCSpectrumButton.show()
if _logger.getEffectiveLevel() == logging.DEBUG:
self.mcafit.configure(config)
else:
try:
thread = CalculationThread.CalculationThread( \
calculation_method = self.mcafit.configure,
calculation_vars = config,
expand_vars=False,
expand_kw=False)
thread.start()
CalculationThread.waitingMessageDialog(thread,
message = "Configuring, please wait",
parent=self,
modal=True,
update_callback=None,
frameless=True)
threadResult = thread.getResult()
if type(threadResult) == type((1,)):
if len(threadResult):
if threadResult[0] == "Exception":
raise Exception(threadResult[1], threadResult[2])
except Exception:
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setWindowTitle("Configuration error")
msg.setText("Error configuring fit:")
msg.setInformativeText(str(sys.exc_info()[1]))
msg.setDetailedText(traceback.format_exc())
msg.exec()
return
#update graph
delcurves = []
curveList = self.graph.getAllCurves(just_legend=True)
for key in curveList:
if key not in ["Data"]:
delcurves.append(key)
for key in delcurves:
self.graph.removeCurve(key)
if not justupdate:
self.plot()
self._updateTop()
if self.concentrationsWidget is not None:
try:
app = qt.QApplication.instance()
app.processEvents()
self.concentrationsWidget.setParameters(config['concentrations'], signal=False)
except Exception:
if str(self.mainTab.tabText(self.mainTab.currentIndex())).upper() == "CONCENTRATIONS":
self.mainTab.setCurrentIndex(0)
def __configureFromConcentrations(self,ddict):
_logger.debug("McaAdvancedFit.__configureFromConcentrations %s", ddict)
config = self.concentrationsWidget.getParameters()
self.mcafit.config['concentrations'].update(config)
if ddict['event'] == 'updated':
if 'concentrations' in ddict:
self._concentrationsDict = ddict['concentrations']
self._concentrationsInfo = None
self._xrfmcMatrixSpectra = None
def __elementclicked(self,ddict):
ddict['event'] = 'McaAdvancedFitElementClicked'
self.__showElementMarker(ddict)
self.__anasignal(ddict)
def __showElementMarker(self, dict):
self.graph.clearMarkers()
ele = dict['current']
items = []
if not (ele in dict):
self.graph.replot()
return
for rays in dict[ele]:
for transition in Elements.Element[ele][rays +" xrays"]:
items.append([transition,
Elements.Element[ele][transition]['energy'],
Elements.Element[ele][transition]['rate']])
config = self.mcafit.configure()
xdata = self.mcafit.xdata * 1.0
xmin = xdata[0]
xmax = xdata[-1]
ymin,ymax = self.graph.getGraphYLimits()
calib = [config['detector'] ['zero'], config['detector'] ['gain']]
for transition,energy,rate in items:
marker = ""
x = (energy - calib[0])/calib[1]
if (x < xmin) or (x > xmax):continue
if not self._energyAxis:
if abs(calib[1]) > 0.0000001:
marker=self.graph.insertXMarker(x,
legend=transition,
text=transition,
color='orange',
replot=False)
else:
marker=self.graph.insertXMarker(energy,
legend=transition,
text=transition,
color='orange',
replot=False)
self.graph.replot()
def _updateTop(self):
config = {}
if 0:
config.update(self.mcafit.config['fit'])
else:
config['stripflag'] = self.mcafit.config['fit'].get('stripflag',0)
config['fitfunction'] = self.mcafit.config['fit'].get('fitfunction',0)
config['hypermetflag'] = self.mcafit.config['fit'].get('hypermetflag',1)
config['sumflag'] = self.mcafit.config['fit'].get('sumflag',0)
config['escapeflag'] = self.mcafit.config['fit'].get('escapeflag',0)
config['continuum'] = self.mcafit.config['fit'].get('continuum',0)
self.top.setParameters(config)
def __updatefromtop(self,ndict):
config = self.mcafit.configure()
for key in ndict.keys():
if key not in ['stripflag', 'hypermetflag',
'sumflag', 'escapeflag',
'fitfunction', 'continuum']:
_logger.debug("UNKNOWN key %s", key)
config['fit'][key] = ndict[key]
self.__fitdone = False
#erase table
if self.mcatable is not None:
self.mcatable.setRowCount(0)
#erase concentrations
if self.concentrationsWidget is not None:
self.concentrationsWidget.concentrationsTable.setRowCount(0)
#erase diagnostics
self.diagnosticsWidget.clear()
#update graph
curveList = self.graph.getAllCurves(just_legend=True)
delcurves = []
for key in curveList:
if key not in ["Data"]:
delcurves.append(key)
for key in delcurves:
self.graph.removeCurve(key)
self.plot()
if _logger.getEffectiveLevel() == logging.DEBUG:
self.mcafit.configure(config)
else:
try:
thread = CalculationThread.CalculationThread( \
calculation_method = self.mcafit.configure,
calculation_vars = config,
expand_vars=False,
expand_kw=False)
thread.start()
CalculationThread.waitingMessageDialog(thread,
message = "Configuring, please wait",
parent=self,
modal=True,
update_callback=None)
threadResult = thread.getResult()
if type(threadResult) == type((1,)):
if len(threadResult):
if threadResult[0] == "Exception":
raise Exception(threadResult[1], threadResult[2])
except Exception:
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setWindowTitle("Configuration error")
msg.setText("Error configuring fit:")
msg.setInformativeText(str(sys.exc_info()[1]))
msg.setDetailedText(traceback.format_exc())
msg.exec()
return
def _tabChanged(self, value):
_logger.debug("_tabChanged(self, value) called")
if str(self.mainTab.tabText(self.mainTab.currentIndex())).upper() == "CONCENTRATIONS":
self.printButton.setEnabled(False)
w = self.concentrationsWidget
if w.parent() is None:
if w.isHidden():
w.show()
w.raise_()
self.printButton.setEnabled(True)
#do not calculate again. It should be already updated
return
try:
self.concentrations()
self.printButton.setEnabled(True)
except Exception:
if _logger.getEffectiveLevel() == logging.DEBUG:
raise
#print "try to set"
self.printButton.setEnabled(False)
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Concentrations error: %s" % sys.exc_info()[1])
msg.exec()
self.mainTab.setCurrentIndex(0)
elif str(self.mainTab.tabText(self.mainTab.currentIndex())).upper() == "TABLE":
self.printButton.setEnabled(True)
w = self.mcatable
if w.parent() is None:
if w.isHidden():
w.show()
w.raise_()
elif str(self.mainTab.tabText(self.mainTab.currentIndex())).upper() == "DIAGNOSTICS":
self.printButton.setEnabled(False)
self.diagnostics()
else:
self.printButton.setEnabled(True)
def _concentrationsWidgetClose(self, ddict):
ddict['info'] = "CONCENTRATIONS"
self._tabReparent(ddict)
def _mcatableClose(self, ddict):
ddict['info'] = "TABLE"
self._tabReparent(ddict)
def _tabReparent(self, ddict):
if ddict['info'] == "CONCENTRATIONS":
w = self.concentrationsWidget
parent = self.tabConcentrations
elif ddict['info'] == "TABLE":
w = self.mcatable
parent = self.tabMca
if w.parent() is not None:
parent.layout().removeWidget(w)
w.setParent(None)
w.show()
else:
w.setParent(parent)
parent.layout().addWidget(w)
def _calibrate(self):
config = self.mcafit.configure()
x = self.mcafit.xdata0[:]
y = self.mcafit.ydata0[:]
legend = "Calibration for " + qt.safe_str(self.headerLabel.text())
ndict={}
ndict[legend] = {'A':config['detector']['zero'],
'B':config['detector']['gain'],
'C': 0.0}
caldialog = McaCalWidget.McaCalWidget(legend=legend,
x=x,
y=y,
modal=1,
caldict=ndict,
fl=0)
caldialog.calpar.orderbox.setEnabled(0)
caldialog.calpar.CText.setEnabled(0)
caldialog.calpar.savebox.setEnabled(0)
ret = caldialog.exec()
if ret == qt.QDialog.Accepted:
ddict = caldialog.getDict()
config['detector']['zero'] = ddict[legend]['A']
config['detector']['gain'] = ddict[legend]['B']
#self.mcafit.configure(config)
self.mcafit.config['detector']['zero'] = 1. * ddict[legend]['A']
self.mcafit.config['detector']['gain'] = 1. * ddict[legend]['B']
self.__fitdone = 0
self.plot()
del caldialog
def __elementsInfo(self):
if self.elementsInfo is None:
self.elementsInfo = ElementsInfo.ElementsInfo(None, "Elements Info")
if self.elementsInfo.isHidden():
self.elementsInfo.show()
self.elementsInfo.raise_()
def __peakIdentifier(self, energy = None):
if energy is None:
energy = 5.9
if self.identifier is None:
self.identifier=PeakIdentifier.PeakIdentifier(energy=energy,
threshold=0.040,
useviewer=1)
self.identifier.mySlot()
self.identifier.setEnergy(energy)
if self.identifier.isHidden():
self.identifier.show()
self.identifier.raise_()
def printActiveTab(self):
txt = str(self.mainTab.tabText(self.mainTab.currentIndex())).upper()
if txt == "GRAPH":
self.graphWindow.printGraph()
elif txt == "TABLE":
self.printps(True)
elif txt == "CONCENTRATIONS":
self.printConcentrations(True)
elif txt == "DIAGNOSTICS":
pass
else:
pass
def diagnostics(self):
self.diagnosticsWidget.clear()
if not self.__fitdone:
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
text = "Sorry. You need to perform a fit first.\n"
msg.setText(text)
msg.exec()
if str(self.mainTab.tabText(self.mainTab.currentIndex())).upper() == "DIAGNOSTICS":
self.mainTab.setCurrentIndex(0)
return
fitresult = self.dict
x = fitresult['result']['xdata']
energy = fitresult['result']['energy']
y = fitresult['result']['ydata']
yfit = fitresult['result']['yfit']
param = fitresult['result']['fittedpar']
i = fitresult['result']['parameters'].index('Noise')
noise= param[i] * param[i]
i = fitresult['result']['parameters'].index('Fano')
fano = param[i] * 2.3548*2.3548*0.00385
meanfwhm = numpy.sqrt(noise + 0.5 * (energy[0] + energy[-1]) * fano)
i = fitresult['result']['parameters'].index('Gain')
gain = fitresult['result']['fittedpar'][i]
meanfwhm = int(meanfwhm/gain) + 1
missed = self.mcafit.detectMissingPeaks(y, yfit, meanfwhm)
hcolor = 'white'
finalcolor = 'white'
text=""
if len(missed):
text+="<br><b><font color=blue size=4>Possibly Missing or Underestimated Peaks</font></b>"
text+="<nobr><table><tr>"
text+='<td align="right" bgcolor="%s"><b>' % hcolor
text+='Channel'
text+="</b></td>"
text+='<td align="right" bgcolor="%s"><b>' % hcolor
text+='Energy'
text+="</b></td>"
text+="</tr>"
for peak in missed:
text+="<tr>"
text+='<td align="right" bgcolor="%s">' % finalcolor
text+="<b><font size=3>%d </font></b>" % x[int(peak)]
text+="</td>"
text+='<td align="right" bgcolor="%s">' % finalcolor
text+="<b><font size=3>%.3f </font></b>" % energy[int(peak)]
text+="</td>"
text+="</tr>"
text+="<tr>"
text+="</table>"
missed = self.mcafit.detectMissingPeaks(yfit, y, meanfwhm)
if len(missed):
text+="<br><b><font color=blue size=4>Possibly Overestimated Peaks</font></b>"
text+="<nobr><table><tr>"
text+='<td align="right" bgcolor="%s"><b>' % hcolor
text+='Channel'
text+="</b></td>"
text+='<td align="right" bgcolor="%s"><b>' % hcolor
text+='Energy'
text+="</b></td>"
text+="</tr>"
for peak in missed:
text+="<tr>"
text+='<td align="right" bgcolor="%s">' % finalcolor
text+="<b><font size=3>%d </font></b>" % x[int(peak)]
text+="</td>"
text+='<td align="right" bgcolor="%s">' % finalcolor
text+="<b><font size=3>%.3f </font></b>" % energy[int(peak)]
text+="</td>"
text+="</tr>"
text+="<tr>"
text+="</table>"
# check for secondary effects
useMatrix = False
for attenuator in fitresult['result']['config']['attenuators']:
if attenuator.upper() == "MATRIX":
if fitresult['result']['config']['attenuators'][attenuator][0]:
useMatrix = True
break
if useMatrix and FISX and \
(not fitresult['result']['config']['concentrations']['usemultilayersecondary']):
doIt = False
corrections = None
if 'fisx' in fitresult['result']['config']:
corrections = fitresult['result']['config']['fisx'].get('corrections',
None)
if corrections is None:
# calculate the corrections
corrections = FisxHelper.getFisxCorrectionFactorsFromFitConfiguration( \
fitresult['result']['config'],
elementsFromMatrix=False)
# to put it into config is misleading because it was not made at
# configuration time.
if 'fisx' not in fitresult['result']['config']:
fitresult['result']['config']['fisx'] = {}
fitresult['result']['config']['fisx']['secondary'] = 2
fitresult['result']['config']['fisx']['corrections'] = corrections
tertiary = False
bodyText = ""
for element in corrections:
for family in corrections[element]:
correction = corrections[element][family]['correction_factor']
if correction[-1] > 1.02:
doIt = True
bodyText += "<tr>"
bodyText += '<td align="right" bgcolor="%s">' % finalcolor
bodyText += "<b><font size=3>%s </font></b>" % \
(element + " " + family)
bodyText += "</td>"
bodyText += '<td align="right" bgcolor="%s">' % finalcolor
bodyText += "<b><font size=3>"
bodyText += "%.3f</font></b>" % correction[1]
bodyText += " "
if len(corrections[element][family]['correction_factor']) > 2:
tertiary = True
bodyText+= "</td>"
bodyText += '<td align="right" bgcolor="%s">' % finalcolor
bodyText += "<b><font size=3>"
bodyText+= "%.3f </font></b>" % correction[2]
bodyText += " "
bodyText+= "</td>"
bodyText+= "</tr>"
if doIt:
bodyText += "<tr>"
bodyText += "</table>"
warningText = "<br><b><font color=blue size=4>"
warningText += "Neglected higher order excitation correction</font></b>"
warningText += "<nobr><table>"
warningText += "<tr>"
warningText += '<td align="right" bgcolor="%s"><b>' % hcolor
warningText += 'Peak Family'
warningText += "</b></td>"
warningText += '<td align="right" bgcolor="%s"><b>' % hcolor
warningText += (' ' * 10)
warningText += '2nd Order'
warningText += "</b></td>"
if tertiary:
warningText += '<td align="right" bgcolor="%s"><b>' % hcolor
warningText += (' ' * 10)
warningText += '3rd Order'
warningText += "</b></td>"
warningText += "</tr>"
text += (warningText + bodyText)
self.diagnosticsWidget.insertHtml(text)
def concentrations(self):
self._concentrationsDict = None
self._concentrationsInfo = None
self._xrfmcMatrixSpectra = None
if not self.__fitdone:
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
text = "Sorry, You need to perform a fit first.\n"
msg.setText(text)
msg.exec()
if str(self.mainTab.tabText(self.mainTab.currentIndex())).upper() == "CONCENTRATIONS":
self.mainTab.setCurrentIndex(0)
return
fitresult = self.dict
if False:
#from the fit, it misses any update from concentrations
config = fitresult['result']['config']
else:
#from current, it should be up to date
config = self.mcafit.configure()
#tool = ConcentrationsWidget.Concentrations(fl=qt.Qt.WDestructiveClose)
if self.concentrationsWidget is None:
self.concentrationsWidget = ConcentrationsWidget.Concentrations()
self.concentrationsWidget.sigConcentrationsSignal.connect( \
self.__configureFromConcentrations)
self.concentrationsWidget.setTimeFactor(self.mcafit.getLastTime(), signal=False)
tool = self.concentrationsWidget
#this forces update
tool.getParameters()
ddict = {}
ddict.update(config['concentrations'])
tool.setParameters(ddict, signal=False)
try:
ddict, info = tool.processFitResult(config=ddict, fitresult=fitresult,
elementsfrommatrix=False,
fluorates=self.mcafit._fluoRates,
addinfo=True)
except Exception:
if _logger.getEffectiveLevel() == logging.DEBUG:
raise
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Error processing fit result: %s" % (sys.exc_info()[1]))
msg.exec()
if str(self.mainTab.tabText(self.mainTab.currentIndex())).upper() == 'CONCENTRATIONS':
self.mainTab.setCurrentIndex(0)
return
self._concentrationsDict = ddict
self._concentrationsInfo = info
tool.show()
tool.setFocus()
tool.raise_()
def __toggleMatrixSpectrum(self):
if self.matrixSpectrumButton.isChecked():
self.matrixSpectrum()
self.plot()
else:
if "Matrix" in self.graph.getAllCurves(just_legend=True):
self.graph.removeCurve("Matrix", replot=False)
self.plot()
def __togglePeaksSpectrum(self):
if self.peaksSpectrumButton.isChecked():
self.peaksSpectrum()
else:
self.__clearPeaksSpectrum()
self.plot()
def __clearPeaksSpectrum(self):
delcurves = []
for key in self.graph.getAllCurves(just_legend=True):
if key not in ["Data", "Fit", "Continuum", "Pile-up", "Matrix"]:
if key.startswith('MC Matrix'):
if self._xrfmcMatrixSpectra in [None, []]:
delcurves.append(key)
else:
delcurves.append(key)
for key in delcurves:
self.graph.removeCurve(key, replot=False)
def matrixSpectrum(self):
if not self.__fitdone:
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
text = "Sorry, for the time being you need to perform a fit first\n"
text+= "in order to calculate the spectrum derived from the matrix.\n"
text+= "Background and detector parameters are taken from last fit"
msg.setText(text)
msg.exec()
return
#fitresult = self.dict['result']
fitresult = self.dict
config = self.mcafit.configure()
self._concentrationsInfo = None
tool = ConcentrationsTool.ConcentrationsTool()
#this forces update
tool.configure()
ddict = {}
ddict.update(config['concentrations'])
tool.configure(ddict)
if _logger.getEffectiveLevel() == logging.DEBUG:
ddict, info = tool.processFitResult(fitresult=fitresult,
elementsfrommatrix=True,
addinfo=True)
else:
try:
thread = CalculationThread.CalculationThread(
calculation_method=tool.processFitResult,
calculation_kw={'fitresult': fitresult,