457 lines
16 KiB
Python
Executable File
457 lines
16 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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from mathlib import fit_anneal, fit_lbfgsb, fit_odr, hn, id_to_color
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from matplotlibWidget import PlotWidget
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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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import PeakWidget
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from data import Data, Conductivity, conductivity
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#import yaff
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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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def tau_peak(f, a, b):
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tau = (N.sin(N.pi * a / 2. / (b + 1)) / N.sin(N.pi * a * b / 2. / (b + 1))) ** (1 / a)
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tau /= 2 * N.pi * f
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return tau
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class Peak(QObject):
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changedData = pyqtSignal()
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def __init__(self, id=None, mpl=None):
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QObject.__init__(self)
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super(Peak, self).__init__()
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self.color = id_to_color(id)
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self.widget = PeakWidget.PeakWidget()
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self.widget.setId(id)
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self.widget.setColor(map(int, [255 * i for i in self.color]))
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self.widget.changedTable.connect(self.updatePeak)
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self.mpl = mpl
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self.mpl_line = None
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def getParameter(self):
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p = self.widget.peakParameter()
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return p
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def getFixed(self):
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p = self.widget.fixedParameter()
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return p
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def setParameter(self, delta_eps=None, tau=None, a=None, b=None):
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self.widget.updateTable(delta_eps, tau, a, b)
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self.updatePeak()
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def updatePeak(self):
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# get current axis limits
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x_min, x_max = self.mpl.canvas.axes.get_xlim()
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y_min, y_max = self.mpl.canvas.axes.get_ylim()
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nu = N.logspace(N.log10(x_min), N.log10(x_max), 2048)
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y = hn(self.getParameter(), nu)
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# clip data to axes limits
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mask = (y < y_max) & (y > y_min)
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y = y[mask]
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nu = nu[mask]
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if self.mpl_line == None:
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self.mpl_line, = self.mpl.canvas.axes.loglog(nu, y, '--', label="Peak %i" % (self.widget.id),
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animated=True) # peak
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self.mpl_line.set_color(self.color)
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else:
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self.mpl_line.set_xdata(nu)
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self.mpl_line.set_ydata(y)
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self.changedData.emit()
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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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# 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)
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# the plot area, a matplotlib widget
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self.mplWidget = PlotWidget(self.ui.mplWidget)
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self.mplWidget.canvas.draw()
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self.mplWidget.updateGeometry()
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# what to do with CIDs?
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self.cid = []
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self.cid.append(self.mplWidget.canvas.mpl_connect("button_press_event", self.mpl_button_press))
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self.cid.append(self.mplWidget.canvas.mpl_connect("pick_event", self.mpl_button_pick))
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self.cid.append(self.mplWidget.canvas.mpl_connect("button_release_event", self.mpl_button_release))
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#self.cid.append(self.mplWidget.canvas.mpl_connect("resize_event", self.myresizeEvent))
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self.mplWidget.toolbar.spanSelectedTrigger.connect(self.set_fit_xlimits)
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def resizeEvent(self, evt):
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"""resizing the main window executes this method
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TODO: FIX RESIZEING keeping mainwindow maximised for now
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:param evt:
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"""
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self.mplWidget.canvas.draw()
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self.mplWidget._bg_cache = self.mplWidget.canvas.copy_from_bbox(self.mplWidget.canvas.axes.bbox)
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for line in self.mplWidget.canvas.axes.get_lines():
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line.set_animated(False)
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self.mplWidget.canvas.draw()
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for line in self.mplWidget.canvas.axes.get_lines():
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line.set_animated(True)
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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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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('# T ')
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parfmt = "%.2f" # T formatting
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# if self.Conductivity != None: pass# always true
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f.write("%8s %8s %8s " % ("e_s", "sig", "pow_sig"))
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parfmt += " %.3g %.3g %.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("%8s %8s %8s %8s " % enum_peak)
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parfmt += " %.3g %.3g %.2f %.2f" # peak formatting
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f.write("high_lim lower_lim") # TODO: store limits
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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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N.savetxt(f, N.array([pars, ]), fmt=parfmt, delimiter=" ")
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f.close()
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def set_fit_xlimits(self, xmin, xmax):
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self.data.fit_limits = (xmin, xmax, None, None)
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self.updatePlot()
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def mpl_button_release(self, event):
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ax = self.mplWidget.canvas.axes
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if self.picked_artist:
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if not event.inaxes: # moved outside the plot, add back to original position
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ax.add_artist(self.picked_artist)
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else: # we move one of the three points determinig the peak
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self.picked_artist.set_xdata(event.xdata)
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self.picked_artist.set_ydata(event.ydata)
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ax.add_artist(self.picked_artist)
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for peak in self.peakBoxes.keys():
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peak.updatePeak()
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self.picked_artist = None
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self.mplWidget.canvas.draw_idle()
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def mpl_button_pick(self, event):
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self.picked_artist = event.artist
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event.artist.remove()
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self.mplWidget.canvas.draw_idle()
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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.mplWidget)
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self.Conductivity.changedData.connect(self.updatePlot)
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self.Conductivity.setParameter(0, 1 / (pos[0] / pos[1] / 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.Conductivity.mpl_line.remove()
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self.Conductivity.mpl_line_static.remove()
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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.mplWidget)
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# connect to delPeak
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peak.widget.ui.removeButton.clicked.connect(self.delPeak)
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peak.setParameter(delta_eps=pos[1], tau=1 / (2. * N.pi * pos[0]), a=1, b=1)
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peak.changedData.connect(self.updatePlot)
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self.peakBoxes[peak] = None
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for pb in self.peakBoxes.keys():
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self.ui.scrollAreaWidgetContents.layout().addWidget(pb.widget)
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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.ui.scrollAreaWidgetContents.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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peak.mpl_line.remove()
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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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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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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 mpl_button_press(self, event):
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"""
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Handles the clicks on the matplotlib figure canvas
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"""
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if self.ui.actionAdd_Peak.isChecked() and event.inaxes:
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x, y = event.xdata, event.ydata
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self.addPeak((x, y))
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self.ui.actionAdd_Peak.setChecked(False)
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self.statusBar().clear()
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if self.ui.actionAdd_Cond.isChecked() and event.inaxes:
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x, y = event.xdata, event.ydata
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self.addCond((x, y))
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self.ui.actionAdd_Cond.setChecked(False)
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self.statusBar().clear()
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def openFile(self):
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ax = self.mplWidget.canvas.axes
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ax.clear()
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path = unicode(QFileDialog.getOpenFileName(self, "Open file"))
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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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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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# clear the figure
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ax.clear()
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#if self.data != None:
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# self.data.remove_curves()
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self.data = Data(_freq, _die_stor, _die_loss)
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self.data.meta["T"] = Temp
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self.data.data_curve, = ax.loglog(self.data.frequency,
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self.data.epsilon.imag,
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'b.',
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markersize=4,
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label="Data",
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animated=True)
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ax.set_xlabel("Frequency/Hz", fontsize=16)
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#ax.set_ylabel(u'\u03B5"', fontsize=16)
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ax.set_ylabel(u'e"', fontsize=16)
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ax.autoscale(True)
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ax.set_xlim(_freq.min()/3, _freq.max()*3)
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self.legend = ax.legend(title="T=%.2f" % Temp)
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for line in ax.get_lines():
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line.set_animated(False)
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ax.grid()
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self.mplWidget.canvas.draw()
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# weird behaviour need to draw all first, then set_animated the redraw
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for line in ax.get_lines():
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line.set_animated(True)
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self.legend.set_animated(True)
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ax.autoscale(False)
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self.mplWidget._bg_cache = self.mplWidget.canvas.copy_from_bbox(ax.bbox)
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self.updatePlot()
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def updatePlot(self):
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ax = self.mplWidget.canvas.axes
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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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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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# clip data to axes limits
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y_min, y_max = ax.get_ylim()
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mask = (fit < y_max) & (fit > y_min)
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#mask = N.ones(len(fit), dtype="bool")
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if self.data.fitted_curve == None:
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self.data.fitted_curve, = ax.loglog(nu[mask], fit[mask],
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'k-',
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alpha=0.5,
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label="Sum",
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animated=True)
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else:
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self.data.fitted_curve.set_xdata(nu[mask])
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self.data.fitted_curve.set_ydata(fit[mask])
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# handling of fit limit bars
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# if self.mplWidget._axvlims != []:
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# [axv.remove() for axv in self.mplWidget._axvlims]
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# self.mplWidget._axvlims = []
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# if self.mplWidget._axvname != []:
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# [axvname.remove() for axvname in self.mplWidget._axvname]
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# self.mplWidget._axvname = []
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#print self.mplWidget._axvlims
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if self.mplWidget._axvlims == []:
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for i,xlim in enumerate(self.data.fit_limits[:2]):
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self.mplWidget._axvlims.append(ax.axvline(xlim, color="k", ls="--", alpha=0.5, animated=True))
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self.mplWidget._axvname.append(ax.text(xlim, y_min*3. , "%.3g"%xlim,
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horizontalalignment='center',
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verticalalignment='center',
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animated=True) )
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else:
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for i,xlim in enumerate(self.data.fit_limits[:2]):
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self.mplWidget._axvlims[i].set_xdata(xlim)
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self.mplWidget._axvname[i].set_x(xlim)
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self.mplWidget._axvname[i].set_text("%.3g"%xlim)
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self.mplWidget.canvas.restore_region(self.mplWidget._bg_cache)
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self.legend = ax.legend(title="T=%.2f" % (self.data.meta["T"]))
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self.legend.set_animated(True)
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for animated_artist in ax.findobj(match=lambda x: x.get_animated()):
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#print "updatePlot: animated artist:",animated_artist
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ax.draw_artist(animated_artist)
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self.mplWidget.canvas.blit(ax.bbox)
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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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