2013-06-14 06:44:34 +00:00
|
|
|
#!/usr/bin/env python
|
|
|
|
# -*- encoding: utf-8 -*-
|
2013-07-10 16:36:07 +00:00
|
|
|
import os
|
|
|
|
import sys
|
2013-06-14 06:44:34 +00:00
|
|
|
import re
|
|
|
|
import signal
|
|
|
|
|
|
|
|
from PyQt4.QtCore import *
|
|
|
|
from PyQt4.QtGui import *
|
2014-02-25 13:55:29 +00:00
|
|
|
import matplotlib
|
2013-06-14 06:44:34 +00:00
|
|
|
|
2014-02-25 13:55:29 +00:00
|
|
|
from mathlib import fit_anneal, fit_lbfgsb, fit_odr, hn
|
2013-07-12 14:11:29 +00:00
|
|
|
|
2014-02-25 13:55:29 +00:00
|
|
|
matplotlib.use('agg')
|
|
|
|
|
|
|
|
#from matplotlibWidget import PlotWidget
|
|
|
|
|
|
|
|
from matplotlib import pyplot
|
|
|
|
from matplotlib.colors import hex2color
|
2013-07-17 11:00:24 +00:00
|
|
|
#matplotlib.rc_file("default.mplrc")
|
2013-06-14 06:44:34 +00:00
|
|
|
|
|
|
|
import numpy as N
|
|
|
|
|
|
|
|
import QDSMain
|
|
|
|
|
2014-02-25 13:55:29 +00:00
|
|
|
from data import Data, Conductivity, conductivity, Peak
|
|
|
|
import pyqtgraph as pg
|
2013-06-14 06:44:34 +00:00
|
|
|
|
2014-02-25 13:55:29 +00:00
|
|
|
#import yaff
|
2013-06-14 06:44:34 +00:00
|
|
|
|
|
|
|
|
|
|
|
class AppWindow(QMainWindow):
|
|
|
|
def __init__(self, parent=None):
|
|
|
|
super(AppWindow, self).__init__(parent)
|
|
|
|
self.ui = QDSMain.Ui_MainWindow()
|
|
|
|
self.ui.setupUi(self)
|
|
|
|
self.picked_artist = None
|
|
|
|
self.data = None
|
|
|
|
|
|
|
|
self.Conductivity = None
|
|
|
|
|
|
|
|
self._lines = dict()
|
|
|
|
|
|
|
|
self.peakId = 0
|
|
|
|
self.peakBoxes = {}
|
2013-07-10 16:36:07 +00:00
|
|
|
|
2013-06-14 06:44:34 +00:00
|
|
|
## menubar
|
|
|
|
fileMenu = self.menuBar().addMenu("File")
|
2013-07-10 16:36:07 +00:00
|
|
|
openFile = QAction("&Open", self)
|
2013-06-14 06:44:34 +00:00
|
|
|
openFile.setShortcut(QKeySequence.Open)
|
|
|
|
openFile.triggered.connect(self.openFile)
|
|
|
|
fileMenu.addAction(openFile)
|
2014-02-25 13:55:29 +00:00
|
|
|
|
|
|
|
saveFile = QAction("&Save Fit Result", self)
|
|
|
|
saveFile.setShortcut(QKeySequence.Save)
|
|
|
|
saveFile.triggered.connect(self.saveFitResult)
|
|
|
|
fileMenu.addAction(saveFile)
|
|
|
|
|
|
|
|
|
2013-06-14 06:44:34 +00:00
|
|
|
# fitting methods
|
2013-07-10 16:36:07 +00:00
|
|
|
fitMenu = self.menuBar().addMenu("Standard Fits")
|
2013-06-14 06:44:34 +00:00
|
|
|
# lm
|
2013-07-10 16:36:07 +00:00
|
|
|
fit_lmAction = QAction("&Levenberg-Marquardt", self)
|
|
|
|
fit_lmAction.setShortcut(QKeySequence("Ctrl+F"))
|
2013-06-14 06:44:34 +00:00
|
|
|
fitMenu.addAction(fit_lmAction)
|
|
|
|
# lbfgsb
|
2013-07-10 16:36:07 +00:00
|
|
|
fit_lbfgsbAction = QAction("&L-BFGS-B", self)
|
2013-06-14 06:44:34 +00:00
|
|
|
fitMenu.addAction(fit_lbfgsbAction)
|
|
|
|
# Simulated Annealing
|
2013-07-10 16:36:07 +00:00
|
|
|
fit_annealAction = QAction("&Simulated Annealing", self)
|
2013-06-14 06:44:34 +00:00
|
|
|
fitMenu.addAction(fit_annealAction)
|
2013-07-10 16:36:07 +00:00
|
|
|
# YAFF
|
|
|
|
yaffMenu = self.menuBar().addMenu("YAFF")
|
|
|
|
start_yaff = QAction("&Startparam.", self)
|
|
|
|
yaffMenu.addAction(start_yaff)
|
|
|
|
fit_yaff = QAction("&Fit", self)
|
|
|
|
yaffMenu.addAction(fit_yaff)
|
2013-06-14 06:44:34 +00:00
|
|
|
|
|
|
|
self.signalMapper = QSignalMapper(self)
|
|
|
|
for i, fit_action in enumerate([fit_lmAction, fit_lbfgsbAction, fit_annealAction
|
2013-07-10 16:36:07 +00:00
|
|
|
]):
|
|
|
|
self.signalMapper.setMapping(fit_action, i)
|
2013-06-14 06:44:34 +00:00
|
|
|
fit_action.triggered.connect(self.signalMapper.map)
|
|
|
|
self.signalMapper.mapped.connect(self.fitData)
|
|
|
|
|
|
|
|
# save fitted values
|
|
|
|
|
2014-02-25 13:55:29 +00:00
|
|
|
#self.ui.actionSave_FitResult.triggered.connect(self.saveFitResult)# replaced by menu
|
|
|
|
|
|
|
|
self.data = Data()
|
|
|
|
|
|
|
|
self.fit_boundary = pg.LinearRegionItem(brush=QColor(254,254,254,10))
|
|
|
|
self.ui.graphicsView.addItem(self.data.data_curve)
|
|
|
|
self.ui.graphicsView.addItem(self.data.fitted_curve)
|
|
|
|
self.ui.graphicsView.addItem(self.fit_boundary)
|
|
|
|
self.ui.graphicsView.setLogMode(x=True, y=True)
|
|
|
|
self.ui.graphicsView.showGrid(x=True, y=True)
|
|
|
|
self.ui.graphicsView.setLabel("bottom","Frequency",units="Hz")
|
|
|
|
self.ui.graphicsView.setLabel("left", "Dielectric loss", units="Debye")
|
|
|
|
self.peak_box_layout = QGridLayout()
|
|
|
|
self.ui.scrollAreaWidgetContents.setLayout(self.peak_box_layout)
|
|
|
|
|
|
|
|
|
|
|
|
def mousePressEvent(self, evt):
|
|
|
|
pos = evt.pos()
|
|
|
|
if self.ui.graphicsView.sceneRect().contains(pos):
|
|
|
|
# translate position to data coordinates
|
|
|
|
data_pos = self.ui.graphicsView.plotItem.vb.mapSceneToView(pos)
|
|
|
|
if self.ui.actionAdd_Peak.isChecked() and not self.ui.actionAdd_Cond.isChecked():
|
|
|
|
self.addPeak(data_pos)
|
|
|
|
self.ui.actionAdd_Peak.setChecked(False)
|
|
|
|
if self.ui.actionAdd_Cond.isChecked() and not self.ui.actionAdd_Peak.isChecked():
|
|
|
|
self.addCond(data_pos)
|
|
|
|
self.ui.actionAdd_Cond.setChecked(False)
|
2013-06-14 06:44:34 +00:00
|
|
|
|
2013-07-17 11:00:24 +00:00
|
|
|
def saveFitResult(self):
|
2013-07-10 16:36:07 +00:00
|
|
|
"""
|
|
|
|
Saving fit parameters to fitresults.log
|
|
|
|
including temperature
|
|
|
|
"""
|
2014-02-25 13:55:29 +00:00
|
|
|
self.saveFitFigure()
|
2013-06-14 06:44:34 +00:00
|
|
|
if not os.path.exists("fitresults.log"):
|
2013-07-10 16:36:07 +00:00
|
|
|
f = open("fitresults.log", "w")
|
2013-06-14 06:44:34 +00:00
|
|
|
else:
|
2013-07-10 16:36:07 +00:00
|
|
|
f = open("fitresults.log", "a")
|
2013-07-17 11:00:24 +00:00
|
|
|
# write header
|
|
|
|
f.write('# T ')
|
|
|
|
parfmt = "%.2f" # T formatting
|
|
|
|
# if self.Conductivity != None: pass# always true
|
|
|
|
f.write("%8s %8s %8s " % ("e_s", "sig", "pow_sig"))
|
|
|
|
parfmt += " %.3g %.3g %.2f " # conductivity formatting
|
|
|
|
for i, pb in enumerate(self.peakBoxes):
|
|
|
|
enum_peak = ("e_inf_%i" % i, "tau_%i" % i, "alpha_%i" % i, "beta_%i" % i)
|
|
|
|
f.write("%8s %8s %8s %8s " % enum_peak)
|
|
|
|
parfmt += " %.3g %.3g %.2f %.2f" # peak formatting
|
|
|
|
f.write("high_lim lower_lim") # TODO: store limits
|
|
|
|
f.write('\n')
|
|
|
|
f.flush()
|
|
|
|
#f.write("%3.2f "%(self.data.meta["T"]))
|
2013-06-14 06:44:34 +00:00
|
|
|
pars = list(self.fitresult)
|
2013-07-10 16:36:07 +00:00
|
|
|
pars.insert(0, self.data.meta["T"])
|
2013-07-17 11:00:24 +00:00
|
|
|
N.savetxt(f, N.array([pars, ]), fmt=parfmt, delimiter=" ")
|
2013-06-14 06:44:34 +00:00
|
|
|
f.close()
|
|
|
|
|
2014-02-25 13:55:29 +00:00
|
|
|
def saveFitFigure(self):
|
|
|
|
fig = pyplot.Figure(figsize=(3.54, 2.75))
|
|
|
|
font = {'family' : 'sans serif',
|
|
|
|
'weight' : 'normal',
|
|
|
|
'size' : 16}
|
|
|
|
|
|
|
|
matplotlib.rc('font', **font)
|
|
|
|
print self.data.epsilon_fit.shape, type(self.data.epsilon_fit)
|
|
|
|
pyplot.loglog(self.data.frequency, self.data.epsilon.imag, 'bo', markersize=4, label="Data")
|
|
|
|
pyplot.loglog(self.data.frequency, self.data.epsilon_fit, 'r-', lw=2, label="Fit")
|
|
|
|
|
|
|
|
for i,peak in enumerate(self.peakBoxes):
|
|
|
|
f,eps = peak.get_data()
|
|
|
|
color = hex2color(str(peak.get_color().name()))
|
|
|
|
pyplot.loglog(f,eps, ls="--", color=color , lw=1.5, label="Peak %i"%i)
|
|
|
|
|
|
|
|
if self.Conductivity != None:
|
|
|
|
f,eps = self.Conductivity.get_conductivity()
|
|
|
|
color = hex2color(str(self.Conductivity.get_color().name()))
|
|
|
|
pyplot.loglog(f,eps, ls="-.", color=color, lw=1.5, label="Cond.")
|
|
|
|
f,eps = self.Conductivity.get_epsilon_static()
|
|
|
|
pyplot.loglog(f,eps, ls=":", color=color, lw=1.5, label=r'$\eps_0$')
|
|
|
|
|
|
|
|
pyplot.legend(title="T=%.1f K"%(self.data.meta["T"]) )
|
|
|
|
pyplot.grid()
|
|
|
|
pyplot.xlabel('f/Hz')
|
|
|
|
pyplot.ylabel('eps"')
|
|
|
|
pyplot.savefig("test.png")
|
|
|
|
fig.clear()
|
|
|
|
|
2013-07-10 16:36:07 +00:00
|
|
|
def set_fit_xlimits(self, xmin, xmax):
|
|
|
|
self.data.fit_limits = (xmin, xmax, None, None)
|
|
|
|
self.updatePlot()
|
2013-06-14 06:44:34 +00:00
|
|
|
|
2013-07-10 16:36:07 +00:00
|
|
|
|
2013-06-14 06:44:34 +00:00
|
|
|
def addCond(self, pos):
|
|
|
|
if self.Conductivity != None:
|
|
|
|
return
|
|
|
|
self.statusBar().showMessage("Click on graph")
|
2014-02-25 13:55:29 +00:00
|
|
|
self.Conductivity = Conductivity(mpl=self.ui.graphicsView, limits=self.data.fit_limits)
|
2013-06-14 06:44:34 +00:00
|
|
|
self.Conductivity.changedData.connect(self.updatePlot)
|
2014-02-25 13:55:29 +00:00
|
|
|
self.Conductivity.setParameter(0, 1 / (10**pos.x() / 10**pos.y() / 2 / N.pi), 1.0)
|
2013-06-14 06:44:34 +00:00
|
|
|
self.ui.scrollAreaWidgetContents.layout().addWidget(self.Conductivity.widget)
|
|
|
|
self.Conductivity.widget.ui.removeButton.clicked.connect(self.delCond)
|
|
|
|
|
|
|
|
def delCond(self):
|
|
|
|
self.cond_param = None
|
|
|
|
self.cond = None
|
2014-02-25 13:55:29 +00:00
|
|
|
self.ui.graphicsView.removeItem(self.Conductivity.mpl_line)
|
|
|
|
self.ui.graphicsView.removeItem(self.Conductivity.mpl_line_static)
|
2013-06-14 06:44:34 +00:00
|
|
|
del self.Conductivity
|
|
|
|
self.Conductivity = None
|
|
|
|
self.updatePlot()
|
|
|
|
|
|
|
|
|
|
|
|
def addPeak(self, pos):
|
|
|
|
self.peakId += 1
|
|
|
|
self.statusBar().showMessage("Select Peak Position")
|
|
|
|
|
2014-02-25 13:55:29 +00:00
|
|
|
peak = Peak(id=self.peakId, mpl=self.ui.graphicsView, limits=self.data.fit_limits)
|
2013-06-14 06:44:34 +00:00
|
|
|
# connect to delPeak
|
|
|
|
peak.widget.ui.removeButton.clicked.connect(self.delPeak)
|
|
|
|
peak.changedData.connect(self.updatePlot)
|
2014-02-25 13:55:29 +00:00
|
|
|
peak.setParameter(delta_eps=10**pos.y(), tau=1 / (10**pos.x()/2/N.pi), a=1, b=1)
|
2013-06-14 06:44:34 +00:00
|
|
|
|
2013-07-10 16:36:07 +00:00
|
|
|
self.peakBoxes[peak] = None
|
2014-02-25 13:55:29 +00:00
|
|
|
wdgt_num = self.peak_box_layout.rowCount()
|
|
|
|
for i,pb in enumerate(self.peakBoxes.keys()):
|
|
|
|
self.peak_box_layout.addWidget(pb.widget, i+wdgt_num, 0)
|
|
|
|
#self.ui.scrollArea.resize()
|
|
|
|
# self.updatePlot()
|
2013-07-10 16:36:07 +00:00
|
|
|
|
2013-06-14 06:44:34 +00:00
|
|
|
def delPeak(self):
|
|
|
|
deletePeaks = []
|
2014-02-25 13:55:29 +00:00
|
|
|
for i in xrange(self.peak_box_layout.count()):
|
2013-06-14 06:44:34 +00:00
|
|
|
print i
|
2013-07-10 16:36:07 +00:00
|
|
|
|
|
|
|
for i, peak in enumerate(self.peakBoxes.keys()):
|
2013-06-14 06:44:34 +00:00
|
|
|
if peak.widget.isHidden():
|
2014-02-25 13:55:29 +00:00
|
|
|
self.ui.graphicsView.removeItem(peak.mpl_line)
|
2013-06-14 06:44:34 +00:00
|
|
|
deletePeaks.append(peak)
|
|
|
|
for peak in deletePeaks:
|
|
|
|
self.peakBoxes.pop(peak)
|
|
|
|
self.updatePlot()
|
|
|
|
|
|
|
|
def fitData(self, method):
|
|
|
|
if self.Conductivity != None:
|
|
|
|
start_parameter = list(self.Conductivity.getParameter())
|
2013-07-10 16:36:07 +00:00
|
|
|
fixed_params = [i for i in self.Conductivity.getFixed()]
|
2013-06-14 06:44:34 +00:00
|
|
|
else:
|
2013-07-10 16:36:07 +00:00
|
|
|
start_parameter = [0, 0, 1]
|
|
|
|
fixed_params = [0, 0, 0]
|
2013-06-14 06:44:34 +00:00
|
|
|
|
|
|
|
for pb in self.peakBoxes.keys():
|
2013-07-10 16:36:07 +00:00
|
|
|
[start_parameter.append(i) for i in pb.getParameter()]
|
|
|
|
[fixed_params.append(i) for i in pb.getFixed()]
|
2013-06-14 06:44:34 +00:00
|
|
|
|
2014-02-25 13:55:29 +00:00
|
|
|
log10fmin, log10fmax = self.fit_boundary.getRegion()
|
|
|
|
xmin,xmax,ymin,ymax = self.data.fit_limits
|
|
|
|
self.data.fit_limits = [10**log10fmin, 10**log10fmax,ymin,ymax]
|
2013-06-14 06:44:34 +00:00
|
|
|
fit_methods = [fit_odr, fit_lbfgsb, fit_anneal]
|
2013-07-10 16:36:07 +00:00
|
|
|
print "StartParameter", start_parameter
|
|
|
|
print "FixedParameter", fixed_params
|
2013-06-14 06:44:34 +00:00
|
|
|
print "Limits (xmin, xmax, ymin, ymax)", self.data.fit_limits
|
|
|
|
_freq, _fit = self.data.get_data()
|
|
|
|
result = fit_methods[method](_freq, _fit.imag, start_parameter, fixed_params)
|
|
|
|
self.fitresult = result
|
2013-07-10 16:36:07 +00:00
|
|
|
for i, pb in enumerate(self.peakBoxes.keys()):
|
|
|
|
delta_eps, tau, a, b = result[3 + i * 4:3 + (i + 1) * 4]
|
|
|
|
pb.setParameter(delta_eps, tau, a, b)
|
|
|
|
e_static, sigma, sigma_N = result[:3]
|
2013-06-14 06:44:34 +00:00
|
|
|
if self.Conductivity != None:
|
2013-07-10 16:36:07 +00:00
|
|
|
self.Conductivity.setParameter(e_static, sigma, sigma_N)
|
|
|
|
#print "*** FIT RESULTS ***"
|
|
|
|
#print u"\u03c3"
|
|
|
|
#print u"\u0394\u03b5"
|
2013-06-14 06:44:34 +00:00
|
|
|
self.updatePlot()
|
2013-07-10 16:36:07 +00:00
|
|
|
|
2013-06-14 06:44:34 +00:00
|
|
|
def openFile(self):
|
|
|
|
path = unicode(QFileDialog.getOpenFileName(self, "Open file"))
|
2014-02-25 13:55:29 +00:00
|
|
|
#path = "MCM42PG0_199.96K.dat"
|
2013-06-14 06:44:34 +00:00
|
|
|
# TODO anaylize file (LF,MF, HF) and act accordingly
|
|
|
|
data = N.loadtxt(path, skiprows=4)
|
2014-02-25 13:55:29 +00:00
|
|
|
self.setWindowTitle(os.path.basename(path))
|
2013-06-14 06:44:34 +00:00
|
|
|
numpat = re.compile('\d+\.\d+')
|
|
|
|
try:
|
2013-07-10 16:36:07 +00:00
|
|
|
Temp = None
|
2013-06-14 06:44:34 +00:00
|
|
|
for line in open(path).readlines():
|
|
|
|
if re.search("Fixed", line) or re.search("Temp", line):
|
2013-07-10 16:36:07 +00:00
|
|
|
print "Found line with Fixed or Temp"
|
2013-06-14 06:44:34 +00:00
|
|
|
Temp = float(re.search(numpat, line).group())
|
2013-07-10 16:36:07 +00:00
|
|
|
print "Temperature found in file:", Temp
|
2013-06-14 06:44:34 +00:00
|
|
|
break
|
2013-07-10 16:36:07 +00:00
|
|
|
if Temp == None: raise ValueError
|
2013-06-14 06:44:34 +00:00
|
|
|
except:
|
2013-07-10 16:36:07 +00:00
|
|
|
Temp = QInputDialog.getDouble(self, "No temperature found in data set", "Temperature/K:", value=0.00)[0]
|
|
|
|
# mask the data to values > 0 (loglog plot)
|
|
|
|
mask = (data[:, 1] > 0) & (data[:, 2] > 0) #& (data[:,2]>1e-3) & (data[:,0] > 1e-2)
|
|
|
|
_freq = data[mask, 0]
|
|
|
|
_die_stor = data[mask, 1]
|
|
|
|
_die_loss = data[mask, 2]
|
2014-02-25 13:55:29 +00:00
|
|
|
self.data.set_data(_freq, _die_stor, _die_loss)
|
2013-07-10 16:36:07 +00:00
|
|
|
self.data.meta["T"] = Temp
|
2014-02-25 13:55:29 +00:00
|
|
|
self.fit_boundary.setRegion([N.log10(_freq.min()), N.log10(_freq.max())])
|
|
|
|
|
2013-06-14 06:44:34 +00:00
|
|
|
self.updatePlot()
|
|
|
|
|
2014-02-25 13:55:29 +00:00
|
|
|
|
2013-06-14 06:44:34 +00:00
|
|
|
def updatePlot(self):
|
|
|
|
nu = self.data.frequency
|
|
|
|
fit = N.zeros(len(nu))
|
|
|
|
for peak in self.peakBoxes.keys():
|
|
|
|
params = peak.getParameter()
|
2013-07-10 16:36:07 +00:00
|
|
|
fit += hn(params, nu)
|
2014-02-25 13:55:29 +00:00
|
|
|
#fit += peak.get_data()[1]
|
2013-06-14 06:44:34 +00:00
|
|
|
if self.Conductivity != None:
|
|
|
|
print "Cond. given"
|
|
|
|
params = self.Conductivity.getParameter()[1:]
|
|
|
|
fit += conductivity(params, nu)
|
|
|
|
fit += self.Conductivity.getParameter()[0] # eps static
|
|
|
|
|
2014-02-25 13:55:29 +00:00
|
|
|
self.data.epsilon_fit = fit[:]
|
|
|
|
self.data.data_curve.setData(self.data.frequency, self.data.epsilon.imag)
|
|
|
|
if len(self.peakBoxes) > 0 and self.Conductivity != None:
|
|
|
|
self.data.fitted_curve.setData(nu, fit)
|
|
|
|
|
|
|
|
|
|
|
|
def sigint_handler(*args):
|
|
|
|
"""Handler for the SIGINT signal (CTRL + C).
|
|
|
|
"""
|
|
|
|
sys.stderr.write('\r')
|
|
|
|
if QMessageBox.question(None, '', "Are you sure you want to quit?",
|
|
|
|
QMessageBox.Yes | QMessageBox.No,
|
|
|
|
QMessageBox.No) == QMessageBox.Yes:
|
|
|
|
QApplication.quit()
|
2013-06-14 06:44:34 +00:00
|
|
|
|
|
|
|
if __name__ == '__main__':
|
|
|
|
signal.signal(signal.SIGINT, sigint_handler)
|
|
|
|
app = QApplication(sys.argv)
|
|
|
|
timer = QTimer()
|
|
|
|
timer.start(1000) # Check every second for Strg-c on Cmd line
|
|
|
|
timer.timeout.connect(lambda: None)
|
|
|
|
main = AppWindow()
|
|
|
|
main.showMaximized()
|
|
|
|
main.raise_()
|
|
|
|
sys.exit(app.exec_())
|