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#/*##########################################################################
#
# The PyMca X-Ray Fluorescence Toolkit
#
# Copyright (c) 2004-2016 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
from PyMca5.PyMcaGui import PyMcaQt as qt
from PyMca5.PyMcaGui import PyMca_Icons
from PyMca5.PyMcaGui import XASNormalizationWindow
from PyMca5.PyMca import XASNormalization
IconDict = PyMca_Icons.IconDict
DEBUG = 0
class XASNormalizationParameters(qt.QGroupBox):
sigNormalizationParametersSignal = qt.pyqtSignal(object)
def __init__(self, parent=None, color=None):
super(XASNormalizationParameters, self).__init__(parent)
self.setTitle("Normalization")
self._dialog = None
self._energy = None
self._mu = None
self.__connected = True
self.build()
if color is not None:
self.setTitleColor(color)
def build(self):
self.mainLayout = qt.QGridLayout(self)
self.mainLayout.setContentsMargins(0, 0, 0, 0)
self.mainLayout.setSpacing(2)
# the normalization method
normalizationLabel = qt.QLabel(self)
normalizationLabel.setText("Method:")
self.normalizationOptions = ["Constant", "Flattened"]
self.normalizationSelector = qt.QComboBox(self)
for option in self.normalizationOptions:
self.normalizationSelector.addItem(option)
self.normalizationSelector.setCurrentIndex(1)
# the E0 value
self.e0CheckBox = qt.QCheckBox(self)
self.e0CheckBox.setText("Auto E0:")
self.e0CheckBox.setChecked(True)
self.e0SpinBox = qt.QDoubleSpinBox(self)
self.e0SpinBox.setMinimum(200.)
self.e0SpinBox.setMaximum(200000.)
self.e0SpinBox.setDecimals(2)
self.e0SpinBox.setSingleStep(0.2)
self.e0SpinBox.setEnabled(False)
# the jump
jumpLabel = qt.QLabel(self)
jumpLabel.setText("Jump:")
self.jumpLine = qt.QLineEdit(self)
self.jumpLine.setEnabled(False)
# the pre-edge
preEdgeLabel = qt.QLabel(self)
preEdgeLabel.setText("Pre-Edge")
self.preEdgeSelector = XASNormalizationWindow.PolynomSelector(self)
self.preEdgeSelector.setCurrentIndex(3)
# pre-edge regions
preEdgeStartLabel = qt.QLabel(self)
preEdgeStartLabel.setText("Begin:")
self.preEdgeStartBox = qt.QDoubleSpinBox(self)
self.preEdgeStartBox.setDecimals(2)
self.preEdgeStartBox.setMinimum(-2000.0)
self.preEdgeStartBox.setMaximum(-5.0)
self.preEdgeStartBox.setValue(-100)
self.preEdgeStartBox.setSingleStep(5.0)
self.preEdgeStartBox.setEnabled(True)
preEdgeEndLabel = qt.QLabel(self)
preEdgeEndLabel.setText("End:")
self.preEdgeEndBox = qt.QDoubleSpinBox(self)
self.preEdgeEndBox.setDecimals(2)
self.preEdgeEndBox.setMinimum(-200.0)
self.preEdgeEndBox.setMaximum(-1.0)
self.preEdgeEndBox.setValue(-40)
self.preEdgeEndBox.setSingleStep(5.0)
self.preEdgeEndBox.setEnabled(True)
# the post-edge
postEdgeLabel = qt.QLabel(self)
postEdgeLabel.setText("Post-Edge")
self.postEdgeSelector = XASNormalizationWindow.PolynomSelector(self)
self.postEdgeSelector.setCurrentIndex(3)
# post-edge regions
postEdgeStartLabel = qt.QLabel(self)
postEdgeStartLabel.setText("Begin:")
self.postEdgeStartBox = qt.QDoubleSpinBox(self)
self.postEdgeStartBox.setDecimals(2)
self.postEdgeStartBox.setMinimum(1.0)
self.postEdgeStartBox.setMaximum(3000.0)
self.postEdgeStartBox.setValue(10)
self.postEdgeStartBox.setSingleStep(5.0)
self.postEdgeStartBox.setEnabled(True)
postEdgeEndLabel = qt.QLabel(self)
postEdgeEndLabel.setText("End:")
self.postEdgeEndBox = qt.QDoubleSpinBox(self)
self.postEdgeEndBox.setDecimals(2)
self.postEdgeEndBox.setMinimum(10.0)
self.postEdgeEndBox.setMaximum(2000.0)
self.postEdgeEndBox.setValue(300)
self.postEdgeEndBox.setSingleStep(5.0)
self.postEdgeEndBox.setEnabled(True)
# arrange everything
self.mainLayout.addWidget(normalizationLabel, 0, 0)
self.mainLayout.addWidget(self.normalizationSelector, 0, 1)
self.mainLayout.addWidget(self.e0CheckBox, 1, 0)
self.mainLayout.addWidget(self.e0SpinBox, 1, 1)
self.mainLayout.addWidget(jumpLabel, 2, 0)
self.mainLayout.addWidget(self.jumpLine, 2, 1)
self.mainLayout.addWidget(preEdgeLabel, 3, 0)
self.mainLayout.addWidget(self.preEdgeSelector, 3, 1)
self.mainLayout.addWidget(preEdgeStartLabel, 4, 0)
self.mainLayout.addWidget(self.preEdgeStartBox, 4, 1)
self.mainLayout.addWidget(preEdgeEndLabel, 5, 0)
self.mainLayout.addWidget(self.preEdgeEndBox, 5, 1)
self.mainLayout.addWidget(postEdgeLabel, 6, 0)
self.mainLayout.addWidget(self.postEdgeSelector, 6, 1)
self.mainLayout.addWidget(postEdgeStartLabel, 7, 0)
self.mainLayout.addWidget(self.postEdgeStartBox, 7, 1)
self.mainLayout.addWidget(postEdgeEndLabel, 8, 0)
self.mainLayout.addWidget(self.postEdgeEndBox, 8, 1)
# connect
self.normalizationSelector.activated[int].connect(self._normalizationChanged)
self.e0CheckBox.toggled.connect(self._e0Toggled)
self.e0SpinBox.valueChanged[float].connect(self._e0Changed)
self.preEdgeSelector.activated[int].connect(self._preEdgeChanged)
self.preEdgeStartBox.valueChanged[float].connect(self._preEdgeStartChanged)
self.preEdgeEndBox.valueChanged[float].connect(self._preEdgeEndChanged)
self.postEdgeSelector.activated[int].connect(self._postEdgeChanged)
self.postEdgeStartBox.valueChanged[float].connect(self._postEdgeStartChanged)
self.postEdgeEndBox.valueChanged[float].connect(self._postEdgeEndChanged)
def _normalizationChanged(self, value):
if DEBUG:
print("_normalizationChanged ", value)
if self.__connected:
self._emitSignal("JumpNormalizationChanged")
def setSpectrum(self, energy, mu):
# try to detect keV
if abs(energy[-1]-energy[0]) < 10:
self._energy = energy * 1000.
else:
self._energy = energy * 1.0
self._mu = mu
try:
self.__connected = False
self._update()
finally:
self.__connected = True
self._emitSignal("SpectrumChanged")
def _calculateE0(self):
return XASNormalization.getE0SavitzkyGolay(self._energy, self._mu,
points=5, full=False)
def _e0Toggled(self, state):
if state:
self.e0SpinBox.setEnabled(False)
if self._mu is not None:
e0 = self._calculateE0()
self.e0SpinBox.setValue(e0)
else:
self.e0SpinBox.setEnabled(True)
def _e0Changed(self, value):
if DEBUG:
print("E0 CHANGED", value)
if self.__connected:
try:
self.__connected = False
self._update()
finally:
self.__connected = True
self._emitSignal("E0Changed")
def _preEdgeChanged(self, value):
if DEBUG:
print("Current pre-edge value = ", value)
if self.__connected:
self._emitSignal("PreEdgeChanged")
def _preEdgeStartChanged(self, value):
if DEBUG:
print("pre start changed", value)
if self.__connected:
try:
self.__connected = False
self._update()
finally:
self.__connected = True
self._emitSignal("PreEdgeChanged")
def _preEdgeEndChanged(self, value):
if DEBUG:
print("pre end changed", value)
if self.__connected:
try:
self.__connected = False
self._update()
finally:
self.__connected = True
self._emitSignal("PreEdgeChanged")
def _postEdgeChanged(self, value):
if DEBUG:
print("post-edge changed", value)
if self.__connected:
self._emitSignal("PostEdgeChanged")
def _postEdgeStartChanged(self, value):
if DEBUG:
print("post-edge start changed", value)
if self.__connected:
try:
self.__connected = False
self._update()
finally:
self.__connected = True
self._emitSignal("PostEdgeChanged")
def _postEdgeEndChanged(self, value):
if DEBUG:
print("post-edge changed", value)
if self.__connected:
try:
self.__connected = False
self._update()
finally:
self.__connected = True
self._emitSignal("PostEdgeChanged")
def _update(self):
if self._energy is None:
return
eMin = self._energy.min()
eMax = self._energy.max()
current = self.getParameters()
if current["E0Method"].lower().startswith("auto") or \
current["E0Value"] < self._energy.min() or \
current["E0Value"] > self._energy.max():
energy = self._calculateE0()
current["E0Value"] = energy
# energy
e0 = current["E0Value"]
self.e0SpinBox.setValue(e0)
# pre-edge
start = e0 + current["PreEdge"]["Regions"][0]
end = e0 + current["PreEdge"]["Regions"][-1]
if start > end:
start, end = end, start
start = max(start, eMin)
if end <= start:
end = 0.5 * (start + energy)
self.preEdgeStartBox.setValue(start - e0)
self.preEdgeEndBox.setValue(end - e0)
# post-edge
start = e0 + current["PostEdge"]["Regions"][0]
end = e0 + current["PostEdge"]["Regions"][-1]
if start > end:
start, end = end, start
end = min(end, eMax)
if end <= start:
start = 0.5 * (end + energy)
self.postEdgeStartBox.setValue(start - e0)
self.postEdgeEndBox.setValue(end - e0)
def getParameters(self):
ddict = {}
# normalization method
ddict["JumpNormalizationMethod"] = str(self.normalizationSelector.currentText())
# default values not yet handled by the interface
ddict["E0MinValue"] = None
ddict["E0MaxValue"] = None
if self.e0CheckBox.isChecked():
ddict["E0Method"] = "Auto - 5pt SG"
else:
ddict["E0Method"] = "Manual"
ddict["E0Value"] = self.e0SpinBox.value()
# pre-edge
ddict["PreEdge"] = {}
ddict["PreEdge"] ["Method"] = "Polynomial"
ddict["PreEdge"] ["Polynomial"] = str(self.preEdgeSelector.currentText())
# Regions is a single list with 2 * n values delimiting n regions.
ddict["PreEdge"] ["Regions"] = [self.preEdgeStartBox.value(),
self.preEdgeEndBox.value()]
ddict["PostEdge"] = {}
ddict["PostEdge"] ["Method"] = "Polynomial"
ddict["PostEdge"] ["Polynomial"] = str(self.postEdgeSelector.currentText())
ddict["PostEdge"] ["Regions"] = [self.postEdgeStartBox.value(),
self.postEdgeEndBox.value()]
return ddict
def setParameters(self, ddict, signal=True):
if DEBUG:
print("setParameters called", ddict, signal)
if "Normalization" in ddict:
ddict = ddict["Normalization"]
try:
self.__connected = False
if "JumpNormalizationMethod" in ddict:
option = ddict["JumpNormalizationMethod"]
if type(ddict["JumpNormalizationMethod"]) == type(1):
self.normalizationSelector.setCurrentIndex(option)
else:
selectorOptions = []
for i in range(self.normalizationSelector.count()):
selectorOptions.append(str(self.normalizationSelector.itemText(i)))
for i in range(len(selectorOptions)):
if selectorOptions[i].lower().startswith(str(option).lower()):
self.normalizationSelector.setCurrentIndex(i)
break
if ddict["E0Value"] is None:
self.e0CheckBox.setChecked(True)
else:
self.e0SpinBox.setValue(ddict["E0Value"])
if ddict["E0Method"].lower().startswith("manual"):
self.e0CheckBox.setChecked(False)
else:
self.e0CheckBox.setChecked(True)
selectorOptions = self.preEdgeSelector.getOptions()
i = 0
for option in selectorOptions:
if str(option) == str(ddict["PreEdge"] ["Polynomial"]):
self.preEdgeSelector.setCurrentIndex(i)
break
i += 1
selectorOptions = self.postEdgeSelector.getOptions()
i = 0
for option in selectorOptions:
if str(option) == str(ddict["PostEdge"] ["Polynomial"]):
self.postEdgeSelector.setCurrentIndex(i)
break
i += 1
self.preEdgeStartBox.setValue(ddict["PreEdge"]["Regions"][0])
self.preEdgeEndBox.setValue(ddict["PreEdge"]["Regions"][-1])
self.postEdgeStartBox.setValue(ddict["PostEdge"]["Regions"][0])
self.postEdgeEndBox.setValue(ddict["PostEdge"]["Regions"][-1])
self._update()
finally:
self.__connected = True
if signal:
# E0Changed or SpectrumUpdated
self._emitSignal("E0Changed")
def _emitSignal(self, event):
ddict = self.getParameters()
ddict["event"] = event
self.jumpLine.setText("")
self.sigNormalizationParametersSignal.emit(ddict)
def setJump(self, value):
self.jumpLine.setText("%f" % value)
def setTitleColor(self, color):
#self.setStyleSheet("QGroupBox {font-weight: bold; color: red;}")
self.setStyleSheet("QGroupBox {color: %s;}" % color)
if __name__ == "__main__":
DEBUG = 1
app = qt.QApplication([])
def mySlot(ddict):
print("Signal received: ", ddict)
w = XASNormalizationParameters()
w.show()
w.sigNormalizationParametersSignal.connect(mySlot)
from PyMca5.PyMcaIO import specfilewrapper as specfile
from PyMca5.PyMcaDataDir import PYMCA_DATA_DIR
if len(sys.argv) > 1:
fileName = sys.argv[1]
else:
fileName = os.path.join(PYMCA_DATA_DIR, "EXAFS_Cu.dat")
data = specfile.Specfile(fileName)[0].data()[-2:, :]
energy = data[0, :]
mu = data[1, :]
w.setSpectrum(energy, mu)
w.setTitleColor("blue")
app.exec_()
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