346 lines
13 KiB
Python
Executable File
346 lines
13 KiB
Python
Executable File
#!/usr/bin/env python
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# -*- encoding: utf-8 -*-
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import os
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import sys
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import re
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import signal
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from PyQt4.QtCore import *
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from PyQt4.QtGui import *
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import matplotlib
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from mathlib import fit_anneal, fit_lbfgsb, fit_odr, hn, FitFunctionCreator, fit_odr_cmplx
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matplotlib.use('agg')
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#from matplotlibWidget import PlotWidget
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from matplotlib import pyplot
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from matplotlib.colors import hex2color
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#matplotlib.rc_file("default.mplrc")
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import numpy as N
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import QDSMain
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from data import Data, Conductivity, conductivity, Peak
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import pyqtgraph as pg
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#import yaff
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class AppWindow(QMainWindow):
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def __init__(self, parent=None):
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super(AppWindow, self).__init__(parent)
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self.ui = QDSMain.Ui_MainWindow()
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self.ui.setupUi(self)
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self.picked_artist = None
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self.data = None
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self.Conductivity = None
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self._lines = dict()
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self.peakId = 0
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self.peakBoxes = {}
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## menubar
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fileMenu = self.menuBar().addMenu("File")
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openFile = QAction("&Open", self)
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openFile.setShortcut(QKeySequence.Open)
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openFile.triggered.connect(self.openFile)
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fileMenu.addAction(openFile)
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saveFile = QAction("&Save Fit Result", self)
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saveFile.setShortcut(QKeySequence.Save)
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saveFile.triggered.connect(self.saveFitResult)
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fileMenu.addAction(saveFile)
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# fitting methods
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fitMenu = self.menuBar().addMenu("Standard Fits")
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# lm
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fit_lmAction = QAction("&Levenberg-Marquardt", self)
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fit_lmAction.setShortcut(QKeySequence("Ctrl+F"))
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fitMenu.addAction(fit_lmAction)
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# lbfgsb
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fit_lbfgsbAction = QAction("&L-BFGS-B", self)
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fitMenu.addAction(fit_lbfgsbAction)
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# Simulated Annealing
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fit_annealAction = QAction("&Simulated Annealing", self)
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fitMenu.addAction(fit_annealAction)
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# YAFF
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yaffMenu = self.menuBar().addMenu("YAFF")
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start_yaff = QAction("&Startparam.", self)
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yaffMenu.addAction(start_yaff)
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fit_yaff = QAction("&Fit", self)
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yaffMenu.addAction(fit_yaff)
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self.signalMapper = QSignalMapper(self)
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for i, fit_action in enumerate([fit_lmAction, fit_lbfgsbAction, fit_annealAction
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]):
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self.signalMapper.setMapping(fit_action, i)
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fit_action.triggered.connect(self.signalMapper.map)
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self.signalMapper.mapped.connect(self.fitData)
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# save fitted values
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#self.ui.actionSave_FitResult.triggered.connect(self.saveFitResult)# replaced by menu
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self.data = Data()
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self.fit_boundary = pg.LinearRegionItem(brush=QColor(254,254,254,10))
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self.ui.graphicsView.addItem(self.data.data_curve_imag)
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self.ui.graphicsView.addItem(self.data.data_curve_real)
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self.ui.graphicsView.addItem(self.data.fitted_curve)
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self.ui.graphicsView.addItem(self.fit_boundary)
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self.ui.graphicsView.setLogMode(x=True, y=True)
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self.ui.graphicsView.showGrid(x=True, y=True)
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self.ui.graphicsView.setLabel("bottom","Frequency",units="Hz")
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self.ui.graphicsView.setLabel("left", "Dielectric loss", units="Debye")
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self.peak_box_layout = QGridLayout()
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self.ui.scrollAreaWidgetContents.setLayout(self.peak_box_layout)
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def mousePressEvent(self, evt):
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pos = evt.pos()
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if self.ui.graphicsView.sceneRect().contains(pos):
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# translate position to data coordinates
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data_pos = self.ui.graphicsView.plotItem.vb.mapSceneToView(pos)
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if self.ui.actionAdd_Peak.isChecked() and not self.ui.actionAdd_Cond.isChecked():
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self.addPeak(data_pos)
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self.ui.actionAdd_Peak.setChecked(False)
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if self.ui.actionAdd_Cond.isChecked() and not self.ui.actionAdd_Peak.isChecked():
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self.addCond(data_pos)
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self.ui.actionAdd_Cond.setChecked(False)
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def saveFitResult(self):
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"""
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Saving fit parameters to fitresults.log
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including temperature
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"""
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self.saveFitFigure()
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if not os.path.exists("fitresults.log"):
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f = open("fitresults.log", "w")
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else:
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f = open("fitresults.log", "a")
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# write header
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f.write("#%7s"%('T'))
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parfmt = "%8.2f" # T formatting
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# if self.Conductivity != None: pass# always true
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f.write("%9s%9s%9s " % ("e_s", "sig", "pow_sig"))
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parfmt += "%9.3g%9.3g%9.2f " # conductivity formatting
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for i, pb in enumerate(self.peakBoxes):
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enum_peak = ("e_inf_%i" % i, "tau_%i" % i, "alpha_%i" % i, "beta_%i" % i)
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f.write("%9s%9s%9s%9s " % enum_peak)
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print enum_peak
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parfmt += "%9.3g%9.3g%9.2f%9.2f" # peak formatting
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f.write("fit_xlow fit_xhigh") # TODO: store limits
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parfmt += "%9.3g%9.3g"
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f.write('\n')
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f.flush()
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#f.write("%3.2f "%(self.data.meta["T"]))
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pars = list(self.fitresult)
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pars.insert(0, self.data.meta["T"])
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pars.append(self.data.fit_limits[0])
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pars.append(self.data.fit_limits[1])
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N.savetxt(f, N.array([pars, ]), fmt=parfmt, delimiter=" ")
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f.close()
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def saveFitFigure(self):
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fig = pyplot.figure(figsize=(3.54, 2.75))
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font = {'family' : 'sans serif',
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'weight' : 'normal',
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'size' : 8}
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matplotlib.rc('font', **font)
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pyplot.loglog(self.data.frequency, self.data.epsilon.imag, 'bo', markersize=3, label="Data")
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pyplot.loglog(self.data.frequency, self.data.epsilon_fit, 'r-', lw=1, label="Fit")
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for i,peak in enumerate(self.peakBoxes):
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f,eps = peak.get_data()
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color = hex2color(str(peak.get_color().name()))
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pyplot.loglog(f,eps, ls="--", color=color , lw=0.75, label="Peak %i"%i)
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if self.Conductivity != None:
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f,eps = self.Conductivity.get_conductivity()
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color = hex2color(str(self.Conductivity.get_color().name()))
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pyplot.loglog(f,eps, ls="-.", color=color, lw=0.75, label="Cond.")
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f,eps = self.Conductivity.get_epsilon_static()
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pyplot.loglog(f,eps, ls=":", color=color, lw=0.75, label=r'$\epsilon_0$')
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for i in (0,1): pyplot.axvline(x=self.data.fit_limits[i], color='g', ls="--")
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pyplot.legend(title = "T=%.1f K"%(self.data.meta["T"]))
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pyplot.grid()
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pyplot.xlabel('f/Hz')
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pyplot.ylabel('eps"')
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pyplot.savefig(os.path.splitext(self.filepath)[0]+".png")
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fig.clear()
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def addCond(self, pos):
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if self.Conductivity != None:
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return
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self.statusBar().showMessage("Click on graph")
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self.Conductivity = Conductivity(mpl=self.ui.graphicsView, limits=self.data.fit_limits)
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self.Conductivity.changedData.connect(self.updatePlot)
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self.Conductivity.setParameter(0, 1 / (10**pos.x() / 10**pos.y() / 2 / N.pi), 1.0)
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self.ui.scrollAreaWidgetContents.layout().addWidget(self.Conductivity.widget)
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self.Conductivity.widget.ui.removeButton.clicked.connect(self.delCond)
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def delCond(self):
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self.cond_param = None
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self.cond = None
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self.ui.graphicsView.removeItem(self.Conductivity.mpl_line)
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self.ui.graphicsView.removeItem(self.Conductivity.mpl_line_static)
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del self.Conductivity
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self.Conductivity = None
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self.updatePlot()
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def addPeak(self, pos):
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self.peakId += 1
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self.statusBar().showMessage("Select Peak Position")
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peak = Peak(id=self.peakId, mpl=self.ui.graphicsView, limits=self.data.fit_limits)
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# connect to delPeak
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peak.widget.ui.removeButton.clicked.connect(self.delPeak)
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peak.changedData.connect(self.updatePlot)
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peak.setParameter(delta_eps=10**pos.y(), tau=1 / (10**pos.x()/2/N.pi), a=1, b=1)
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self.peakBoxes[peak] = None
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wdgt_num = self.peak_box_layout.rowCount()
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for i,pb in enumerate(self.peakBoxes.keys()):
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self.peak_box_layout.addWidget(pb.widget, i+wdgt_num, 0)
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#self.ui.scrollArea.resize()
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# self.updatePlot()
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def delPeak(self):
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deletePeaks = []
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for i in xrange(self.peak_box_layout.count()):
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print i
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for i, peak in enumerate(self.peakBoxes.keys()):
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if peak.widget.isHidden():
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self.ui.graphicsView.removeItem(peak.mpl_line)
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deletePeaks.append(peak)
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for peak in deletePeaks:
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self.peakBoxes.pop(peak)
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self.updatePlot()
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def fitData(self, method):
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if self.Conductivity != None:
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start_parameter = list(self.Conductivity.getParameter())
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fixed_params = [i for i in self.Conductivity.getFixed()]
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else:
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start_parameter = [0, 0, 1]
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fixed_params = [0, 0, 0]
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for pb in self.peakBoxes.keys():
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[start_parameter.append(i) for i in pb.getParameter()]
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[fixed_params.append(i) for i in pb.getFixed()]
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log10fmin, log10fmax = self.fit_boundary.getRegion()
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self.data.set_fit_xlimits(10**log10fmin, 10**log10fmax)
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fit_methods = [fit_odr, fit_lbfgsb, fit_anneal]
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print "StartParameter", start_parameter
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print "FixedParameter", fixed_params
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print "Limits (xmin, xmax, ymin, ymax)", self.data.fit_limits
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_freq, _fit = self.data.get_data()
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result = fit_methods[method](_freq, _fit.imag, start_parameter, fixed_params)
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# check new method
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if 1:
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funcs = ["static","conductivity"] if self.Conductivity != None else []
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for pb in self.peakBoxes.keys():
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funcs.append("hn")
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newres = fit_odr_cmplx(_freq, _fit, start_parameter, fixed_params, funcs)
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print newres
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self.fitresult = result
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for i, pb in enumerate(self.peakBoxes.keys()):
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delta_eps, tau, a, b = result[3 + i*4 : 3 + (i + 1)*4]
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pb.setParameter(delta_eps, tau, a, b)
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e_static, sigma, sigma_N = result[:3]
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if self.Conductivity != None:
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self.Conductivity.setParameter(e_static, sigma, sigma_N)
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#print "*** FIT RESULTS ***"
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#print u"\u03c3"
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#print u"\u0394\u03b5"
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self.updatePlot()
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def openFile(self):
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path = unicode(QFileDialog.getOpenFileName(self, "Open file"))
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self.filepath=path
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#path = "MCM42PG0_199.96K.dat"
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# TODO anaylize file (LF,MF, HF) and act accordingly
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data = N.loadtxt(path, skiprows=4)
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self.setWindowTitle(os.path.basename(path))
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numpat = re.compile('\d+\.\d+')
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try:
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Temp = None
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for line in open(path).readlines():
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if re.search("Fixed", line) or re.search("Temp", line):
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print "Found line with Fixed or Temp"
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Temp = float(re.search(numpat, line).group())
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print "Temperature found in file:", Temp
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break
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if Temp == None: raise ValueError
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except:
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Temp = QInputDialog.getDouble(self, "No temperature found in data set", "Temperature/K:", value=0.00)[0]
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# mask the data to values > 0 (loglog plot)
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mask = (data[:, 1] > 0) & (data[:, 2] > 0) #& (data[:,2]>1e-3) & (data[:,0] > 1e-2)
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_freq = data[mask, 0]
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_die_stor = data[mask, 1]
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_die_loss = data[mask, 2]
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self.data.set_data(_freq, _die_stor, _die_loss)
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self.data.meta["T"] = Temp
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self.fit_boundary.setRegion([N.log10(_freq.min()), N.log10(_freq.max())])
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self.updatePlot()
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def updatePlot(self):
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nu = self.data.frequency
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fit = N.zeros(len(nu))
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for peak in self.peakBoxes.keys():
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params = peak.getParameter()
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fit += hn(params, nu)
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#fit += peak.get_data()[1]
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if self.Conductivity != None:
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print "Cond. given"
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params = self.Conductivity.getParameter()[1:]
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fit += conductivity(params, nu)
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fit += self.Conductivity.getParameter()[0] # eps static
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self.data.epsilon_fit = fit[:]
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self.data.data_curve_imag.setData(self.data.frequency, self.data.epsilon.imag)
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self.data.data_curve_imag.setData(self.data.frequency, self.data.epsilon.real)
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if len(self.peakBoxes) > 0 and self.Conductivity != None:
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self.data.fitted_curve.setData(nu, fit)
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def sigint_handler(*args):
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"""Handler for the SIGINT signal (CTRL + C).
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"""
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sys.stderr.write('\r')
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if QMessageBox.question(None, '', "Are you sure you want to quit?",
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QMessageBox.Yes | QMessageBox.No,
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QMessageBox.No) == QMessageBox.Yes:
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QApplication.quit()
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if __name__ == '__main__':
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signal.signal(signal.SIGINT, sigint_handler)
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app = QApplication(sys.argv)
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timer = QTimer()
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timer.start(1000) # Check every second for Strg-c on Cmd line
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timer.timeout.connect(lambda: None)
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main = AppWindow()
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main.showMaximized()
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main.raise_()
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sys.exit(app.exec_())
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