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xaesaGUI.py
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xaesaGUI.py
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# -*- coding: utf-8 -*-
#"""
#Created on Fri Oct 7 12:25:31 2016
#
#@author: sasha
#"""
XAESA_VERSION = "0.07"
GUI_SETTINGS_ID = "XAESA" + XAESA_VERSION
import sys
from sys import exit, argv, version
from os import path, getcwd, getpid
import matplotlib.pyplot as plt
from matplotlib import __version__ as mpl_version
__path__=[path.dirname(path.abspath(__file__))]
from .init import QTVer
from .xaesa_exafs_class import xaesa_exafs_class
from .xaesa_xes_class import xaesa_xes_class, xaesa_transient_class
from .xaesa_settings import xaesa_settings
from .xaesa_viewer import xaesa_viewer, xaesaViewerWindow
from .xaesa_rxes import xaesa_rxes, xaesaRxesWindow
import modified_widgets as modwid
import tooltiptexts as ttt
import h5py
import copy as c
def show_exception_and_exit(exc_type, exc_value, tb):
import traceback
traceback.print_exception(exc_type, exc_value, tb)
# raw_input("Press key to exit.")
# sys.exit(-1)
sys.excepthook = show_exception_and_exit
if QTVer == 4:
from PyQt4 import QtGui, QtCore
from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.backends.backend_qt4agg import NavigationToolbar2QT as NavigationToolbar
print("Python version: " + str(version))
print("Qt version: " + str(QtCore.qVersion()))
print("MatPlotLib version: " + str(mpl_version))
print("h5py version: " + h5py.version.version)
print("HDF5 version: " + h5py.version.hdf5_version)
if QTVer == 5:
from PyQt5 import QtWidgets as QtGui
from PyQt5 import QtCore
from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as NavigationToolbar
print("Python version: " + str(version))
print("Qt version: " + str(QtCore.qVersion()))
print("MatPlotLib version: " + str(mpl_version))
print("h5py version: " + h5py.version.version)
print("HDF5 version: " + h5py.version.hdf5_version)
from numpy import asarray, fromstring, genfromtxt, gradient, argmax, zeros, sqrt, sin, transpose, \
array, savetxt, copy, delete, arange, exp, argmin, concatenate, all, diff, \
append, where, absolute, logical_and, reshape, max, min, average, sum
#from .ft import FT, BFTWindow, BFT, GETPHASE
#from scipy.interpolate import UnivariateSpline
from scipy.interpolate import Rbf #, UnivariateSpline
from scipy.interpolate import InterpolatedUnivariateSpline
from timeit import default_timer as timer
from .xaesa_deglitch import DGWindow
from .xaesa_fit import FitWindow
from .xaesa_rdf import RdfWindow, MyStream
from .compare import CompareWindow
from .xaesa_lincombination import LCWindow
from .xaesa_pca import PCAWindow
from scipy.integrate import simps
#from matplotlib.widgets import RectangleSelector
polPowerXES = 1
def format_coord(x, y):
return 'x=%1.4f, y=%1.4f' % (x, y)
class MyWindow(QtGui.QMainWindow):
# def resizeEvent(self,resizeEvent):
#
# print("Information!","Window has been resized...")
def __init__(self):
super(MyWindow, self).__init__()
self.exafs_fluo = 0 #0 - exafs, 1 - fluo
self.calcmju = 1 #calculate mju or take already calculated from file
self.skiplines = 0
self.energycol = 0
self.exafscol = 1
self.refcol = -1
self.i0col = 1
self.i1col = 2
self.i2col = -1
self.fluocol = [11,12,13,15,16,17]
self.setWindowTitle("XAESA - X-ray Absorption and Emission Analytics")
self.dataClasses = []
self.copiedparamsXAS = []
self.copiedparamsXES = []
self.initUI()
self.showMaximized()
def initUI(self):
exitAction = QtGui.QAction('&Exit', self)
exitAction.setShortcut('Ctrl+Q')
exitAction.setStatusTip('Exit application')
exitAction.triggered.connect(QtGui.qApp.quit)
savehdf5Action = QtGui.QAction('Save analysis &to hdf5 ...', self)
savehdf5Action.setShortcut('Ctrl+S')
savehdf5Action.triggered.connect(self.savehdf5)
openhdf5Action = QtGui.QAction('Open analysis &from hdf5 ...', self)
openhdf5Action.setShortcut('Ctrl+A')
openhdf5Action.triggered.connect(self.openhdf5)
openNexusAction = QtGui.QAction('Open Nexus file ...', self)
openNexusAction.setShortcut('Ctrl+N')
openNexusAction.triggered.connect(self.openNexus)
ampPhaSaveAction = QtGui.QAction('Save amplitude and phase ...', self)
ampPhaSaveAction.triggered.connect(self.ampPhaSave)
# rxesAction = QtGui.QAction('Plot RXES plane ...', self)
# rxesAction.triggered.connect(self.makeRxesPlane, lambda: self.compare('i0'))
menubar = self.menuBar()
fileMenu = menubar.addMenu('&File')
fileMenu.addAction(savehdf5Action)
fileMenu.addAction(openhdf5Action)
fileMenu.addAction(openNexusAction)
fileMenu.addAction(exitAction)
toolsMenu = menubar.addMenu('&Tools')
toolsMenu.addAction(ampPhaSaveAction)
toolsMenu.addAction('Plot RXES plane ...', lambda: self.makeRxesPlane(False))
toolsMenu.addAction('Plot RXES plane (energy transfer) ...', lambda: self.makeRxesPlane(True))
toolsMenu.addAction('Shift energy scale according reference (last selected spectrum)', self.shiftEnergyRef)
settingsMenu = menubar.addMenu('&Settings')
self.xaesaSettings = xaesa_settings()
# self.edtTest = QtGui.QLineEdit('1')
action = QtGui.QWidgetAction(self)
action.setDefaultWidget(self.xaesaSettings)
settingsMenu.addAction(action)
statusBar = self.statusBar()
self.prgbar = QtGui.QProgressBar()
self.lblStatus = QtGui.QLabel("Start with opening experimental files or previously saved project.")
self.lblnpoints = QtGui.QLabel()
self.lblCurrentFile = QtGui.QLabel()
statusBar.addWidget(self.lblStatus)
statusBar.addWidget(self.prgbar)
statusBar.addWidget(self.lblnpoints)
statusBar.addWidget(self.lblCurrentFile)
self.current = -1
self.currentdir = getcwd()
self.currenthdf5 = getcwd()
wid = QtGui.QWidget(self)
self.setCentralWidget(wid)
#list with spectra
#from several text files or single hdf5 file
self.lstSpectra = QtGui.QListWidget()
self.lstSpectra.itemClicked.connect(self.lstSpectraItemClicked)
self.lstSpectra.itemDoubleClicked.connect(self.lstSpectraItemDoubleClicked)
self.lstSpectra.itemActivated.connect(self.lstSpectraItemClicked)
self.lstSpectra.setSelectionMode(QtGui.QAbstractItemView.ExtendedSelection)
# self.lstSpectra.setDragDropMode(QtGui.QAbstractItemView.DragDrop)
self.lstSpectra.setDragDropMode(QtGui.QAbstractItemView.InternalMove)
self.lstSpectra.setDefaultDropAction(QtCore.Qt.MoveAction)
self.lstSpectra.installEventFilter(self)
# self.lstSpectra.indexesMoved.connect(self.lstSpectraLayoutChanged)
# self.lstSpectraModel = self.lstSpectra.model()
# self.lstSpectraModel.layoutChanged.connect(self.lstSpectraLayoutChanged)
self.lstSpectra.setContextMenuPolicy(QtCore.Qt.CustomContextMenu)
self.lstSpectra.customContextMenuRequested.connect(self.listItemRightClicked)
self.lstSpectraMenu= QtGui.QMenu()
self.lstSpectraMenu.addAction("Remove Item", self.removefile)
self.lstSpectraMenu.addSeparator()
self.lstSpectraMenu.addAction("DW factor correction", self.dwcorrection)
self.lstSpectraMenu.addAction("Shift energy scale by constant", self.shiftenergyscale)
self.lstSpectraMenu.addSeparator()
self.lstSpectraMenu.addAction("Compare mu", self.comparemju)
self.lstSpectraMenu.addAction("Compare EXAFS", self.compareexafs)
self.lstSpectraMenu.addAction("Compare FT", self.compareft)
self.lstSpectraMenu.addAction("Compare BFT", self.comparebft)
self.lstSpectraMenu.addSeparator()
self.lstSpectraMenu.addAction("Spectra difference", self.spectradifference)
self.lstSpectraMenu.addSeparator()
self.lstSpectraMenu.addAction("Duplicate", self.duplicate)
#open button
self.btnOpen = QtGui.QPushButton('Open File(s) ...')
self.btnRemoveFile = QtGui.QPushButton('Remove File(s) ...')
self.btnOpen.clicked.connect(self.openfile)
self.btnRemoveFile.clicked.connect(self.removefile)
self.lblSkipLines = QtGui.QLabel("Skip lines")
self.lblDataX = QtGui.QLabel("Energy")
self.lblDataY = QtGui.QLabel("mu")
self.lblDataY1 = QtGui.QLabel("mu ref")
self.lblI0Col = QtGui.QLabel("I0")
self.lblI1Col = QtGui.QLabel("I1")
self.lblI2Col = QtGui.QLabel("I2")
# self.lblFluoCols = QtGui.QLabel("Fluo columns")
self.edtSkipLines = QtGui.QLineEdit(str(self.skiplines))
self.edtEnergyCol = QtGui.QLineEdit(str(self.energycol))
self.edtExafsCol = QtGui.QLineEdit(str(self.exafscol))
self.edtRefCol = QtGui.QLineEdit(str(self.refcol))
self.edtI0Col = QtGui.QLineEdit(str(self.i0col))
self.edtICol = QtGui.QLineEdit(str(self.i1col))
self.edtI2Col = QtGui.QLineEdit(str(self.i2col))
self.edtFluoCols = QtGui.QLineEdit("11 12 13 15 16 17")
self.edtFluoCols.hide()
self.edtSkipLines.setFixedWidth(50)
self.edtSkipLines.setSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Fixed)
self.edtEnergyCol.setFixedWidth(50)
self.edtEnergyCol.setSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Fixed)
self.edtExafsCol.setFixedWidth(50)
self.edtExafsCol.setSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Fixed)
self.edtRefCol.setFixedWidth(50)
self.edtRefCol.setSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Fixed)
self.edtI0Col.setFixedWidth(50)
self.edtI0Col.setSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Fixed)
self.edtICol.setFixedWidth(50)
self.edtICol.setSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Fixed)
self.edtI2Col.setFixedWidth(50)
self.edtI2Col.setSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Fixed)
# self.edtFluoCols.setFixedWidth(175)
# self.edtFluoCols.setSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Fixed)
g1 = QtGui.QHBoxLayout()
g2 = QtGui.QHBoxLayout()
g3 = QtGui.QHBoxLayout()
self.gb1 = QtGui.QGroupBox()
self.gb2 = QtGui.QGroupBox()
self.gb3 = QtGui.QGroupBox()
self.gb1.setLayout(g1)
self.gb2.setLayout(g2)
self.gb3.setLayout(g3)
self.gb1.setFlat(True)
self.gb2.setFlat(True)
self.gb3.setFlat(True)
#experiment type
self.chkDataTypeMju = QtGui.QPushButton("mu")
self.chkDataTypeXes = QtGui.QPushButton("XES")
self.chkDataTypeExafs = QtGui.QPushButton("EXAFS")
self.chkDataTypeTrans = QtGui.QPushButton("Transient")
self.chkDataTypeTrans.setVisible(False)
self.chkDataTypeMju.setCheckable(True)
self.chkDataTypeXes.setCheckable(True)
self.chkDataTypeExafs.setCheckable(True)
self.chkDataTypeTrans.setCheckable(True)
self.chkDataTypeMju.setAutoExclusive(True)
self.chkDataTypeXes.setAutoExclusive(True)
self.chkDataTypeExafs.setAutoExclusive(True)
self.chkDataTypeTrans.setAutoExclusive(True)
self.chkDataTypeMju.setStyleSheet("QPushButton:checked { color:green }")
self.chkDataTypeXes.setStyleSheet("QPushButton:checked { color:green }")
self.chkDataTypeExafs.setStyleSheet("QPushButton:checked { color:green }")
self.chkDataTypeTrans.setStyleSheet("QPushButton:checked { color:green }")
self.chkDataTypeMju.clicked.connect(self.adaptOpeningParams)
self.chkDataTypeXes.clicked.connect(self.adaptOpeningParams)
self.chkDataTypeExafs.clicked.connect(self.adaptOpeningParams)
self.chkDataTypeTrans.clicked.connect(self.adaptOpeningParams)
# self.chkMjuOrExafs = QtGui.QPushButton("Absorption")
# self.chkMjuOrExafs1 = QtGui.QPushButton("EXAFS")
self.chkCalcMju = QtGui.QPushButton("Calculate absorption")
self.chkCalcMju.setCheckable(True)
self.chkCalcMju.setStyleSheet("QPushButton:checked { color:green }")
self.chkCalcMju.clicked.connect(self.adaptOpeningParams)
self.chkTransOrFluo = QtGui.QPushButton("Transmission")
self.chkTransOrFluo1 = QtGui.QPushButton("Fluorescence")
self.chkTransOrFluo.clicked.connect(self.adaptOpeningParams)
self.chkTransOrFluo1.clicked.connect(self.adaptOpeningParams)
self.chkTransOrFluo.setCheckable(True)
self.chkTransOrFluo1.setCheckable(True)
# self.chkMjuOrExafs.setCheckable(True)
# self.chkMjuOrExafs1.setCheckable(True)
self.chkTransOrFluo.setAutoExclusive(True)
self.chkTransOrFluo1.setAutoExclusive(True)
# self.chkMjuOrExafs.setAutoExclusive(True)
# self.chkMjuOrExafs1.setAutoExclusive(True)
self.chkTransOrFluo.setStyleSheet("QPushButton:checked { color:green }")
self.chkTransOrFluo1.setStyleSheet("QPushButton:checked { color:green }")
# self.chkMjuOrExafs.setStyleSheet("QPushButton:checked { color:green }")
# self.chkMjuOrExafs1.setStyleSheet("QPushButton:checked { color:green }")
self.chkTransOrFluo.setChecked(True)
self.chkDataTypeMju.setChecked(True)
g1.addWidget(self.chkDataTypeMju)
g1.addWidget(self.chkDataTypeXes)
g1.addWidget(self.chkDataTypeExafs)
g1.addWidget(self.chkDataTypeTrans)
g2.addWidget(self.chkCalcMju)
g3.addWidget(self.chkTransOrFluo)
g3.addWidget(self.chkTransOrFluo1)
lopenparams = QtGui.QGridLayout()
lopenparams.addWidget(self.gb1, 0, 0, 1, 8)
lopenparams.addWidget(self.lblSkipLines, 1, 0, alignment=QtCore.Qt.AlignRight)
lopenparams.addWidget(self.edtSkipLines, 1, 1, alignment=QtCore.Qt.AlignLeft)
lopenparams.addWidget(self.lblDataX, 1, 2, alignment=QtCore.Qt.AlignRight)
lopenparams.addWidget(self.edtEnergyCol, 1, 3, alignment=QtCore.Qt.AlignLeft)
lopenparams.addWidget(self.lblDataY, 1, 4, alignment=QtCore.Qt.AlignRight)
lopenparams.addWidget(self.edtExafsCol, 1, 5, alignment=QtCore.Qt.AlignLeft)
lopenparams.addWidget(self.lblDataY1, 1, 6, alignment=QtCore.Qt.AlignRight)
lopenparams.addWidget(self.edtRefCol, 1, 7, alignment=QtCore.Qt.AlignLeft)
lopenparams.addWidget(self.gb2, 2, 0, 1, 3)
lopenparams.addWidget(self.gb3, 2, 3, 1, 5)
lopenparams.addWidget(self.lblI0Col, 3, 0, alignment=QtCore.Qt.AlignRight)
lopenparams.addWidget(self.edtI0Col, 3, 1, alignment=QtCore.Qt.AlignLeft)
lopenparams.addWidget(self.lblI1Col, 3, 2, alignment=QtCore.Qt.AlignRight)
lopenparams.addWidget(self.edtICol, 3, 3, 1, 3, alignment=QtCore.Qt.AlignLeft)
lopenparams.addWidget(self.lblI2Col, 3, 6, alignment=QtCore.Qt.AlignRight)
lopenparams.addWidget(self.edtI2Col, 3, 7, alignment=QtCore.Qt.AlignLeft)
lopenparams.addWidget(self.edtFluoCols, 3, 3, 1, 3, alignment=QtCore.Qt.AlignLeft)
lh = QtGui.QHBoxLayout()
l1 = QtGui.QVBoxLayout()
lh.addWidget(self.btnOpen)
lh.addWidget(self.btnRemoveFile)
l1.addLayout(lh)
l1.addLayout(lopenparams)
l1.addWidget(self.lstSpectra)
##################### XAS FIGURES
#Figures
self.fig = plt.figure(0)
self.ax_abs2 = plt.subplot2grid((2,3), (0,0), fig=self.fig)
self.ax_abs = self.ax_abs2.twinx()
#init lines
self.abs_scatter, = self.ax_abs.plot([], [], 'o', picker=True)
self.abs_scatter.set_markersize(2)
self.mjub_line, self.mju0_mjub_line = self.ax_abs.plot([], [], [], [])
self.mjub_line.set_color('orange')
self.mju0_mjub_line.set_color('orange')
self.deriv_line, = self.ax_abs2.plot([],[])
self.deriv_line.set_color('b')
self.deriv_line.set_alpha(0.3)
self.lineEs = self.ax_abs.axvline(0, color='firebrick', linestyle='--',
lw=2,
picker=True,
pickradius=2)
self.lineE0 = self.ax_abs.axvline(0, color='deeppink', linestyle='--',
lw=2,
picker=True,
pickradius=2)
self.lineE1 = self.ax_abs.axvline(0, color='olive', linestyle='--',
lw=2,
picker=True,
pickradius=2)
self.lineE2 = self.ax_abs.axvline(0, color='steelblue', linestyle='--',
lw=2,
picker=True,
pickradius=2)
self.lineE3 = self.ax_abs.axvline(0, color='purple', linestyle='--',
lw=2,
picker=True,
pickradius=2)
# drag and drop E lines
# self.c = self.ax_abs.get_figure().canvas
# self.sid = self.c.mpl_connect('pick_event', self.pick_a_line)
self.fig.canvas.mpl_connect('pick_event', self.pick_a_line)
self.ax_abs.set_xlabel('Energy, eV')
self.ax_abs.set_ylabel('Absorption, a.u.')
self.ax_exafs = plt.subplot2grid((2,3), (1,0), fig=self.fig)
self.exafs_line, = self.ax_exafs.plot([], [], label = "EXAFS")
self.exafs_line.set_color('k')
self.exafssm_line, = self.ax_exafs.plot([], [], label = "zlc")
self.exafssm_line.set_color('r')
self.ax_exafs_legend = self.ax_exafs.legend(handles=[self.exafs_line, self.exafssm_line])
self.ax_exafs.axhline(y=0, linewidth=1, color = 'k')
self.ax_exafssm = plt.subplot2grid((2,3), (0,1), colspan=2, fig=self.fig)
self.ax_exafssm.axhline(y=0, linewidth=1, color = 'k')
self.exafsd_line, = self.ax_exafssm.plot([], [], label = "EXAFS zlc")
self.bftexafs_line, = self.ax_exafssm.plot( [], [], label = "BFT")
self.bftexafs_line.set_color('r')
self.ax_exafs.set_xlabel('Wavevector k, $\AA^{-1}$')
self.ax_exafs.set_ylabel('EXAFS, $\AA^{-2}$')
self.ax_exafssm.set_xlabel('Wavevector k, $\AA^{-1}$')
self.ax_exafssm.set_ylabel('EXAFS, $\AA^{-2}$')
self.ax_exafsm_legend = self.ax_exafssm.legend(handles=[self.exafsd_line, self.bftexafs_line])
self.ax_ft = plt.subplot2grid((2,3), (1,1), colspan=2, fig=self.fig)
self.efr_line, self.efi_line = self.ax_ft.plot( [], [], [], [], label = "FT")
self.efr_line.set_color('g')
self.efi_line.set_color('g')
self.efi_line.set_linestyle('dotted')
self.efrsm_line, self.efism_line = self.ax_ft.plot([], [], [], [], label = "FT zlc")
self.efrsm_line.set_color('b')
self.efism_line.set_color('b')
self.efism_line.set_linestyle('dotted')
self.bftwinr_line, self.bftwini_line = self.ax_ft.plot([], [], [], [], label = "BFT FT")
self.bftwinr_line.set_color('r')
self.bftwini_line.set_color('r')
self.bftwini_line.set_linestyle('dotted')
self.ax_ft_legend = self.ax_ft.legend(handles=[self.efr_line, self.efrsm_line, self.bftwinr_line])
self.canv = FigureCanvas(self.fig)
self.tbar = NavigationToolbar(self.canv, self)
fnt = self.tbar.font()
fnt.setPointSize(20)
self.tbar.setFont(fnt)
self.ax_ft.set_xlabel('Distance R, $\AA$')
self.ax_ft.set_ylabel('Fourier transform, $\AA^{-3}$')
self.fig.tight_layout()
# self.fig.canvas.mpl_connect('pick_event', self.onpick3)
self.ax_ft.axhline(y=0, linewidth=1, color = 'k')
lfig = QtGui.QVBoxLayout()
lfig.addWidget(self.tbar)
lfig.addWidget(self.canv)
#Frame for xas figures
self.frameXasFig = QtGui.QFrame()
self.frameXasFig.setFrameShape(QtGui.QFrame.Panel)
self.frameXasFig.setFrameShadow(QtGui.QFrame.Sunken)
self.frameXasFig.setLayout(lfig)
self.frameXasFig.hide()
#XAS FIGURES END
### XES FIGURES
self.figXes = plt.figure(11)
self.ax_xes = plt.subplot2grid((2,2), (0,0))
#init lines
#self.abs_scatter = self.ax_abs.scatter([], [], s=1, picker=True)
self.lineXesOriginal, = self.ax_xes.plot([], [], 'o', picker=True)
self.lineXesOriginal.set_markersize(2)
self.lineXesBkgr, = self.ax_xes.plot([], [])
self.lineXesBkgr.set_color('g')
self.lineE0xes = self.ax_xes.axvline(0, color='g', linestyle='--', lw=1)
self.lineE1xes = self.ax_xes.axvline(0, color='g', linestyle='--', lw=1)
self.lineE2xes = self.ax_xes.axvline(0, color='g', linestyle='--', lw=1)
self.lineE3xes = self.ax_xes.axvline(0, color='g', linestyle='--', lw=1)
self.lineEminAnorm = self.ax_xes.axvline(0, color='r', linestyle='--', lw=1)
self.lineEmaxAnorm = self.ax_xes.axvline(0, color='r', linestyle='--', lw=1)
self.ax_xes.set_xlabel('Energy, eV')
self.ax_xes.set_ylabel('Emission intensity, a.u.')
# self.ax_xes.format_coord = format_coord
self.ax_xes_bc = plt.subplot2grid((2,2), (0,1))
self.lineXesBkgrCorr, = self.ax_xes_bc.plot([], []) #, label = "EXAFS")
self.lineXesBkgrCorr.set_color('k')
# self.exafssm_line, = self.ax_xes_bc.plot([], []) #, label = "zlc")
# self.exafssm_line.set_color('r')
# self.ax_exafs.legend(handles=[self.exafs_line, self.exafssm_line])
self.ax_xes_bc.axhline(y=0, linewidth=1, color = 'k')
self.ax_xes_norm = plt.subplot2grid((2,2), (1,0), colspan=2)
self.ax_xes_norm.axhline(y=0, linewidth=1, color = 'k')
self.lineXesNorm, = self.ax_xes_norm.plot([], []) #, label = "EXAFS zlc")
self.canvXes = FigureCanvas(self.figXes)
self.tbarXes = NavigationToolbar(self.canvXes, self)
fnt = self.tbarXes.font()
fnt.setPointSize(20)
self.tbarXes.setFont(fnt)
# self.ax_ft.set_xlabel('Distance R, $\AA$')
# self.ax_ft.set_ylabel('Fourier transform, $\AA^{-3}$')
self.figXes.tight_layout()
# self.figXes.canvas.mpl_connect('pick_event', self.onpick3)
# self.ax_ft.axhline(y=0, linewidth=1, color = 'k')
#
lfig = QtGui.QVBoxLayout()
lfig.addWidget(self.tbarXes)
lfig.addWidget(self.canvXes)
#Frame for XES figures
self.frameXesFig = QtGui.QFrame()
self.frameXesFig.setFrameShape(QtGui.QFrame.Panel)
self.frameXesFig.setFrameShadow(QtGui.QFrame.Sunken)
self.frameXesFig.setLayout(lfig)
# self.frameXesFig.hide()
#XES FIGURES END
###################### XES parameters
lblE0xes = QtGui.QLabel("E0")
lblE1xes = QtGui.QLabel("E1")
lblE2xes = QtGui.QLabel("E2")
lblE3xes = QtGui.QLabel("E3")
lblEMinANormxes = QtGui.QLabel("Emin for area norm")
lblEAMaxNormxes = QtGui.QLabel("Emax for area norm")
self.edtXesE0 = QtGui.QLineEdit()
self.edtXesE1 = QtGui.QLineEdit()
self.edtXesE2 = QtGui.QLineEdit()
self.edtXesE3 = QtGui.QLineEdit()
self.edtXesEANormMin = QtGui.QLineEdit()
self.edtXesEANormMax = QtGui.QLineEdit()
self.edtXesE0.returnPressed.connect(self.xesExtractRedo)
self.edtXesE1.returnPressed.connect(self.xesExtractRedo)
self.edtXesE2.returnPressed.connect(self.xesExtractRedo)
self.edtXesE3.returnPressed.connect(self.xesExtractRedo)
self.edtXesEANormMin.returnPressed.connect(self.xesExtractRedo)
self.edtXesEANormMax.returnPressed.connect(self.xesExtractRedo)
lparams = QtGui.QGridLayout()
lparams.addWidget(lblE0xes, 0, 0)
lparams.addWidget(lblE1xes, 1, 0)
lparams.addWidget(lblE2xes, 2, 0)
lparams.addWidget(lblE3xes, 3, 0)
lparams.addWidget(self.edtXesE0, 0, 1)
lparams.addWidget(self.edtXesE1, 1, 1)
lparams.addWidget(self.edtXesE2, 2, 1)
lparams.addWidget(self.edtXesE3, 3, 1)
lparams.addWidget(lblEMinANormxes, 0, 2)
lparams.addWidget(lblEAMaxNormxes, 1, 2)
lparams.addWidget(self.edtXesEANormMin, 0, 3)
lparams.addWidget(self.edtXesEANormMax, 1, 3)
self.frameXesParams = QtGui.QFrame()
self.frameXesParams.setFrameShape(QtGui.QFrame.Panel)
self.frameXesParams.setFrameShadow(QtGui.QFrame.Sunken)
self.frameXesParams.setLayout(lparams)
self.frameXesParams.hide()
###################### XES traansient parameters
lblEMinSmoothTrans = QtGui.QLabel("Emin for smoothing")
lblEMaxSmoothTrans = QtGui.QLabel("Emax for smoothing")
lblSmoothFactor = QtGui.QLabel("Smoothing factor")
self.edtEMinSmoothTrans = QtGui.QLineEdit()
self.edtEMaxSmoothTrans = QtGui.QLineEdit()
self.edtSmoothFactor = QtGui.QLineEdit()
lblInt1 = QtGui.QLabel("Transient integral")
lblInt2 = QtGui.QLabel("Smoothed transient integral")
lblError = QtGui.QLabel("Difference")
self.edtInt1Show = QtGui.QLineEdit("")
self.edtInt2Show = QtGui.QLineEdit("")
self.edtErrorShow = QtGui.QLineEdit("")
self.edtEMinSmoothTrans.returnPressed.connect(self.transChange)
self.edtEMaxSmoothTrans.returnPressed.connect(self.transChange)
self.edtSmoothFactor.returnPressed.connect(self.transChange)
lparams = QtGui.QGridLayout()
lparams.addWidget(lblEMinSmoothTrans, 0, 0)
lparams.addWidget(lblEMaxSmoothTrans, 1, 0)
lparams.addWidget(lblSmoothFactor, 2, 0)
lparams.addWidget(self.edtEMinSmoothTrans, 0, 1)
lparams.addWidget(self.edtEMaxSmoothTrans, 1, 1)
lparams.addWidget(self.edtSmoothFactor, 2, 1)
lparams.addWidget(lblInt1, 0, 2)
lparams.addWidget(lblInt2, 1, 2)
lparams.addWidget(lblError, 2, 2)
lparams.addWidget(self.edtInt1Show, 0, 3)
lparams.addWidget(self.edtInt2Show, 1, 3)
lparams.addWidget(self.edtErrorShow, 2, 3)
self.frameTransParams = QtGui.QFrame()
self.frameTransParams.setFrameShape(QtGui.QFrame.Panel)
self.frameTransParams.setFrameShadow(QtGui.QFrame.Sunken)
self.frameTransParams.setLayout(lparams)
self.frameTransParams.hide()
#XES parameters END
#Energy params
self.lblEs = QtGui.QLabel("Es")
self.lblE0 = QtGui.QLabel("E0")
self.lblE1 = QtGui.QLabel("E1")
self.lblE2 = QtGui.QLabel("E2")
self.lblE3 = QtGui.QLabel("E3")
self.chkExafsNormalization = QtGui.QCheckBox("Normalize by edge at energy")
self.chkReduceK = QtGui.QCheckBox("Reduce k points (averaging)")
self.chkReduceK.clicked.connect(self.extractParamsChange)
self.lblkpow = QtGui.QLabel("k^n")
self.lblEnergyShift = QtGui.QLabel("Energy scale shift")
self.lblsm = QtGui.QLabel("Zero-line correction (zlc)")
self.lblmju0poldegree = QtGui.QLabel("Mu0 polynomial")
self.lblBckgDegree = QtGui.QLabel("Backgr polynomial (-1 - Vectoreen)")
self.edtEs = modwid.QLineEditScroll()
self.edtE0 = modwid.QLineEditScroll()
self.edtE1 = modwid.QLineEditScroll()
self.edtE2 = modwid.QLineEditScroll()
self.edtE3 = modwid.QLineEditScroll()
self.edtExafsNormEnergy = QtGui.QLineEdit()
self.edtkpow = QtGui.QLineEdit("2")
self.edtEnergyShift = QtGui.QLineEdit("0")
self.edtEnergyShift.setEnabled(False)
self.edtsm = QtGui.QLineEdit("0")
self.edtmju0poldegree = QtGui.QLineEdit("4")
self.edtbckgdegree = QtGui.QLineEdit("-1")
self.btnDeglitching = QtGui.QPushButton('Remove glitches ...')
self.btnDeglitching.clicked.connect(self.removeglitches)
self.lblEs.setStyleSheet("color:#B22222;");
self.lblE0.setStyleSheet("color:#FF1493;");
self.lblE1.setStyleSheet("color:#808000;");
self.lblE2.setStyleSheet("color:#4682B4;");
self.lblE3.setStyleSheet("color:#800080;");
self.edtEs.setToolTip(ttt.xas_es)
self.edtE3.setToolTip(ttt.xas_e3)
lparams = QtGui.QGridLayout()
lparams1 = QtGui.QHBoxLayout()
lparams1.addWidget(self.lblEs)
lparams1.addWidget(self.edtEs)
lparams1.addWidget(self.lblE0)
lparams1.addWidget(self.edtE0)
lparams1.addWidget(self.lblE1)
lparams1.addWidget(self.edtE1)
lparams1.addWidget(self.lblE2)
lparams1.addWidget(self.edtE2)
lparams1.addWidget(self.lblE3)
lparams1.addWidget(self.edtE3)
lparams.addLayout(lparams1, 0,0,1,4)
lparams.addWidget(self.chkExafsNormalization, 1, 0)
lparams.addWidget(self.edtExafsNormEnergy, 1, 1)
lparams.addWidget(self.chkReduceK, 1, 2, 1, 2)
lparams2 = QtGui.QHBoxLayout()
lparams2.addWidget(self.lblsm)
lparams2.addWidget(self.edtsm)
lparams2.addWidget(self.lblkpow)
lparams2.addWidget(self.edtkpow)
lparams2.addWidget(self.lblEnergyShift)
lparams2.addWidget(self.edtEnergyShift)
lparams.addLayout(lparams2, 2,0,1,4)
lparams3 = QtGui.QHBoxLayout()
lparams3.addWidget(self.lblmju0poldegree)
lparams3.addWidget(self.edtmju0poldegree)
lparams3.addWidget(self.lblBckgDegree)
lparams3.addWidget(self.edtbckgdegree)
lparams3.addWidget(self.btnDeglitching)
lparams.addLayout(lparams3, 3,0,1,4)
self.edtEs.returnPressed.connect(self.extractParamsChange)
self.edtE0.returnPressed.connect(self.extractParamsChange)
self.edtE1.returnPressed.connect(self.extractParamsChange)
self.edtE2.returnPressed.connect(self.extractParamsChange)
self.edtE3.returnPressed.connect(self.extractParamsChange)
self.edtkpow.returnPressed.connect(self.kPowerChange)
self.edtsm.returnPressed.connect(self.extractParamsChange)
self.edtmju0poldegree.returnPressed.connect(self.extractParamsChange)
self.edtbckgdegree.returnPressed.connect(self.extractParamsChange)
self.edtExafsNormEnergy.returnPressed.connect(self.extractParamsChange)
#Frame for lparams
self.frameLParams = QtGui.QFrame()
self.frameLParams.setFrameShape(QtGui.QFrame.Panel)
self.frameLParams.setFrameShadow(QtGui.QFrame.Sunken)
self.frameLParams.setLayout(lparams)
self.lblkmin = QtGui.QLabel("K min")
self.lblkmax = QtGui.QLabel("K max")
self.lbldk = QtGui.QLabel("dK ")
self.lblrmin = QtGui.QLabel("R min")
self.lblrmax = QtGui.QLabel("R max")
self.lbldr = QtGui.QLabel("dR ")
self.edtkmin = QtGui.QLineEdit("0.5")
self.edtkmax = QtGui.QLineEdit("18")
self.edtdk = QtGui.QLineEdit("0.05")
self.edtrmin = QtGui.QLineEdit("0")
self.edtrmax = QtGui.QLineEdit("6")
self.edtdr = QtGui.QLineEdit("0.02")
self.edtkmin.returnPressed.connect(self.ftBftParamsChange)
self.edtkmax.returnPressed.connect(self.ftBftParamsChange)
self.edtdk.returnPressed.connect(self.ftBftParamsChange)
self.edtrmin.returnPressed.connect(self.ftBftParamsChange)
self.edtrmax.returnPressed.connect(self.ftBftParamsChange)
self.edtdr.returnPressed.connect(self.ftBftParamsChange)
lftparams = QtGui.QGridLayout()
lftparams.addWidget(self.lblkmin, 0, 0)
lftparams.addWidget(self.lblkmax, 0, 1)
lftparams.addWidget(self.lbldk, 0, 2)
lftparams.addWidget(self.edtkmin, 1, 0)
lftparams.addWidget(self.edtkmax, 1, 1)
lftparams.addWidget(self.edtdk, 1, 2)
lftparams.addWidget(self.lblrmin, 2, 0)
lftparams.addWidget(self.lblrmax, 2, 1)
lftparams.addWidget(self.lbldr, 2, 2)
lftparams.addWidget(self.edtrmin, 3, 0)
lftparams.addWidget(self.edtrmax, 3, 1)
lftparams.addWidget(self.edtdr, 3, 2)
#Frame for lftparams
self.frameLFTParams = QtGui.QFrame()
self.frameLFTParams.setFrameShape(QtGui.QFrame.Panel)
self.frameLFTParams.setFrameShadow(QtGui.QFrame.Sunken)
self.frameLFTParams.setLayout(lftparams)
self.lblrminbft = QtGui.QLabel("BFT R min")
self.lblrmaxbft = QtGui.QLabel("BFT R max")
self.lblbftwindowparam = QtGui.QLabel("BFT window param")
self.edtrminbft = QtGui.QLineEdit("0")
self.edtrmaxbft = QtGui.QLineEdit("6")
self.edtbftwindowparam = QtGui.QLineEdit("0.1")
self.edtrminbft.returnPressed.connect(self.bftParamsChange)
self.edtrmaxbft.returnPressed.connect(self.bftParamsChange)
self.edtbftwindowparam.returnPressed.connect(self.bftParamsChange)
self.btnFit = QtGui.QPushButton('Fit 1st sphere ...')
self.btnFit.clicked.connect(self.fit)
self.btnRdf = QtGui.QPushButton('Reconstruct RDF ...')
self.btnRdf.clicked.connect(self.rdf)
lbftparams = QtGui.QGridLayout()
lbftparams.addWidget(self.lblrminbft, 0,0)
lbftparams.addWidget(self.lblrmaxbft, 0,1)
lbftparams.addWidget(self.lblbftwindowparam, 0,2)
lbftparams.addWidget(self.edtrminbft, 1,0)
lbftparams.addWidget(self.edtrmaxbft, 1,1)
lbftparams.addWidget(self.edtbftwindowparam, 1,2)
lbftparams.addWidget(self.btnFit, 2,0, 1, 3)
lbftparams.addWidget(self.btnRdf, 3,0, 1, 3)
#Frame for lbftparams
self.frameLBFTParams = QtGui.QFrame()
self.frameLBFTParams.setFrameShape(QtGui.QFrame.Panel)
self.frameLBFTParams.setFrameShadow(QtGui.QFrame.Sunken)
self.frameLBFTParams.setLayout(lbftparams)
#compare buttons
self.mnuCompareXAS = QtGui.QMenu()
self.mnuCompareXAS.addAction('Compare mu...', self.comparemju)
self.mnuCompareXAS.addAction('Compare XANES...', self.comparexanes)
self.mnuCompareXAS.addAction('Compare EXAFS...', self.compareexafs)
self.mnuCompareXAS.addAction('Compare FT...', self.compareft)
self.mnuCompareXAS.addAction('Compare BFT...', self.comparebft)
self.mnuCompareXAS.addSeparator()
self.mnuCompareXAS.addAction('Compare i0', lambda: self.compare('i0'))
self.mnuCompareXAS.addAction('Compare i1', lambda: self.compare('i1'))
self.mnuCompareXAS.addAction('Compare i2', lambda: self.compare('i2'))
self.mnuCompareXAS.addAction('Compare i fluorescence', lambda: self.compare('ifluo'))
self.mnuCompareXAS.addAction('Compare mu ref', lambda: self.compare('muref'))
self.mnuCompareXAS.addSeparator()
self.mnuCompareXAS.addAction('Compare amplitude', lambda: self.compare('amp'))
self.mnuCompareXAS.addAction('Compare phase', lambda: self.compare('pha'))
self.mnuCompareXAS.addSeparator()
self.mnuCompareXAS.addAction('Compare mu rebin vs original', lambda: self.compare('mjuRebinVSoriginal'))
#
self.mnuCompareXES = QtGui.QMenu()
self.mnuCompareXES.addAction('Compare XES...', self.compareXes)
self.mnuCompareXES.addAction('Compare XES area normalized...', self.compareXesAnorm)
self.btnCompareXas = QtGui.QPushButton('Compare ...')
# self.btnCompareXas.setMenu(self.mnuCompareXAS)
#save buttons
self.mnuSaveXAS = QtGui.QMenu()
self.mnuSaveXAS.addAction('Save mu...', self.savemju)
self.mnuSaveXAS.addAction('Save XANES...', self.savexanes)
self.mnuSaveXAS.addAction('Save EXAFS...', self.saveexafs)
self.mnuSaveXAS.addAction('Save FT...', self.saveft)
self.mnuSaveXAS.addAction('Save BFT...', self.savebft)
self.mnuSaveXES = QtGui.QMenu()
self.mnuSaveXES.addAction('Save XES...', self.saveXes)
self.mnuSaveXES.addAction('Save XES area normalized...', self.saveXesAnorm)
self.btnSaveXas = QtGui.QPushButton('Save ...')
# self.btnSaveXas.setMenu(self.mnuSaveXAS)
lh = QtGui.QHBoxLayout()
lh.addWidget(self.btnCompareXas)
lh.addWidget(self.btnSaveXas)
l1.addLayout(lh)
self.chkSaveinOneFile = QtGui.QCheckBox("Save selected in single file")
self.chkSaveinOneFile.setChecked(False)
l1.addLayout(lh)
l1.addWidget(self.chkSaveinOneFile)
self.btnAverage = QtGui.QPushButton('Average / merge')
self.mnuAverageXAS = QtGui.QMenu()
self.mnuAverageXAS.addAction('Average mu direct', self.averageMjuDirect)
self.mnuAverageXAS.addAction('Average mu spline', self.averageMjuSpline)
self.mnuAverageXAS.addAction('Average EXAFS', self.averageExafs)
self.mnuAverageXAS.addAction('Merge mu', self.mergeMju)
self.mnuAverageXES = QtGui.QMenu()
self.mnuAverageXES.addAction('Average XES', self.averageXes)
self.btnRebin = QtGui.QPushButton('Rebin')
self.mnuRebinXAS = QtGui.QMenu()
self.mnuRebinXAS.addAction('Rebin mu', self.rebinMju)
self.mnuRebinXAS.addAction('Return to original mu', self.backToOriginalMju)
# self.mnuRebinXAS.addSeparator()
# self.mnuRebinXAS.addAction('Rebin EXAFS', self.rebinExafs)
self.mnuRebinXES = QtGui.QMenu()
self.mnuRebinXES.addAction('Rebin XES', self.rebinXes)
self.btnLinCombination = QtGui.QPushButton('Linear combination...')
self.btnLinCombination.clicked.connect(self.LinCombination)
self.btnPCA = QtGui.QPushButton('PCA analysis...')
self.btnPCA.clicked.connect(self.pcaAnalysis)
self.btnPCA.setEnabled(False)
# self.chkPicker = QtGui.QCheckBox("Allow to remove experimental points")
# self.chkPicker.stateChanged.connect(self.redraw_for_remove)
self.btnCopyParams = QtGui.QPushButton('Copy params')
self.btnCopyParams.clicked.connect(self.CopyParams)
self.btnApplytoSelected = QtGui.QPushButton('Apply params to selected')
self.btnApplytoSelected.clicked.connect(self.ApplytoSelected)
lh1 = QtGui.QHBoxLayout()
lh1.addWidget(self.btnCopyParams)
lh1.addWidget(self.btnApplytoSelected)
lbtn = QtGui.QGridLayout()
lbtn.addLayout(lh1, 0, 0, 1, 2)
lbtn.addWidget(self.btnAverage, 1, 0)
lbtn.addWidget(self.btnRebin, 1, 1)
lbtn.addWidget(self.btnLinCombination, 2, 0, 1, 2)
lbtn.addWidget(self.btnPCA, 3, 0, 1, 2)
layout = QtGui.QGridLayout()
layout.addLayout(l1, 0, 0)
layout.addWidget(self.frameXasFig, 0, 1, 1,3)
layout.addWidget(self.frameXesFig, 0, 1, 1,3)
layout.addLayout(lbtn, 1, 0)
layout.addWidget(self.frameLParams, 1, 1)
layout.addWidget(self.frameXesParams, 1, 1)
layout.addWidget(self.frameTransParams, 1, 1)
layout.addWidget(self.frameLFTParams, 1, 2)
layout.addWidget(self.frameLBFTParams, 1, 3)
layout.setColumnStretch(0,1)
layout.setColumnStretch(1,1)
layout.setColumnStretch(2,1)
layout.setColumnStretch(3,1)
lftparams.setAlignment(QtCore.Qt.AlignTop)
lbftparams.setAlignment(QtCore.Qt.AlignTop)
wid.setLayout(layout)
self.initialdir = ""
self.fig.tight_layout()
# self.fig.canvas.mpl_connect('pick_event', self.onpick)
self.canv.draw()
self.adaptOpeningParams()