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#/*##########################################################################
# Copyright (C) 2004-2014 V.A. Sole, 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.A. Sole - ESRF Data Analysis"
__contact__ = "sole@esrf.fr"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
import numpy
from PyMca5 import Plugin1DBase
from PyMca5.PyMcaPhysics.xas import XASSelfattenuationCorrection
from PyMca5.PyMcaGui.physics.xas import XASSelfattenuationWindow
class XASSelfattenuationPlugin(Plugin1DBase.Plugin1DBase):
def __init__(self, plotWindow, **kw):
Plugin1DBase.Plugin1DBase.__init__(self, plotWindow, **kw)
self.methodDict = {}
text = "Configure fluorescent XAS self-\n"
text += "attenuation correction parameters.\n"
text += "Input curves need to be normalized.\n"
text += "For the time being thick sample is assumed."
function = self.configure
info = text
icon = None
self.methodDict["Configure"] =[function,
info,
icon]
function = self.correctActive
text = "Add corrected active curve."
info = text
icon = None
self.methodDict["Correct Active"] =[function,
info,
icon]
function = self.correctAll
text = "Replace all curves by normalized ones."
info = text
icon = None
self.methodDict["Correct All"] =[function,
info,
icon]
self.widget = None
self.instance = XASSelfattenuationCorrection.XASSelfattenuationCorrection()
self.parameters = None
self.configuration = None
#Methods to be implemented by the plugin
def getMethods(self, plottype=None):
"""
A list with the NAMES associated to the callable methods
that are applicable to the specified plot.
Plot type can be "SCAN", "MCA", None, ...
"""
names = list(self.methodDict.keys())
names.sort()
return names
def getMethodToolTip(self, name):
"""
Returns the help associated to the particular method name or None.
"""
return self.methodDict[name][1]
def getMethodPixmap(self, name):
"""
Returns the pixmap associated to the particular method name or None.
"""
return self.methodDict[name][2]
def applyMethod(self, name):
"""
The plugin is asked to apply the method associated to name.
"""
self.methodDict[name][0]()
return
def configure(self):
if self.widget is None:
self.widget = XASSelfattenuationWindow.XASSelfattenuationDialog()
ret = self.widget.exec()
if ret:
self.configuration = self.widget.getConfiguration()
self.instance.setConfiguration(self.configuration)
def correctActive(self):
#check we have a configuration
if self.configuration is None:
raise RuntimeError("Please configure the plugin")
#get active curve
activeCurve = self.getActiveCurve()
if activeCurve is None:
raise ValueError("Please select an active curve")
return
energy, spectrum, legend, info = activeCurve[0:4]
spectrum = self.instance.correctNormalizedSpectrum(energy, spectrum)
self.addCurve(energy, spectrum, legend="CORR"+legend, info=info, replace=False, replot=True)
def correctAll(self):
#check we have a configuration
if self.configuration is None:
raise RuntimeError("Please configure the plugin")
curves = self.getAllCurves()
nCurves = len(curves)
if nCurves < 1:
raise ValueError("At least one curve needed")
return
#get active curve
activeCurve = self.getActiveCurve()
if activeCurve is None:
activeCurve = curves[0]
for i in range(nCurves):
energy, spectrum, legend, info = curves[i][0:4]
if i == 0:
replace = True
else:
replace = False
if i == nCurves - 1:
replot = True
else:
replot = False
spectrum = self.instance.correctNormalizedSpectrum(energy, spectrum)
self.addCurve(energy, spectrum, legend="CORR"+legend, info=info,
replot=replot, replace=replace)
MENU_TEXT = "XAS Self-Attenuation Correction"
def getPlugin1DInstance(plotWindow, **kw):
ob = XASSelfattenuationPlugin(plotWindow)
return ob
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