564 lines
21 KiB
Python
Executable File
564 lines
21 KiB
Python
Executable File
#!/usr/bin/env python
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# -*- encoding: utf-8 -*-
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_author_ = "Markus Rosenstihl"
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import hashlib, uuid
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import time
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import os, sys, re, signal
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import matplotlib
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matplotlib.use('agg')
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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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from PyQt4.QtCore import *
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from PyQt4.QtGui import *
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import numpy as np
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import pyqtgraph as pg
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from data.container import Conductivity, PowerComplex, Static, Peak, YAFF
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from gui.container_widgets import ParameterWidget
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from ui import QDSMain
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from libmath.BDSlib import FunctionRegister, FitRoutine
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from data.experimental import Data
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from gui import ExtraDifferentialWidget
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from bds_io import bds_file_reader
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class AppWindow(QMainWindow):
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def __init__( self, files=[], 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._file_paths = self._sortInputFiles(files)
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self._last_written_header = None
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# create action group
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actions = {
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self.ui.actionAdd_Peak: True,
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self.ui.actionAdd_Cond: True,
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self.ui.actionAdd_PowerLaw: True,
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self.ui.actionAdd_Eps_Infty: True,
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self.ui.actionYAFF: True,
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}
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self.myActionGroup = QActionGroup(self)
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for a in actions.keys(): self.myActionGroup.addAction(a)
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self._init_menu()
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self.function_registry = FunctionRegister()
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self.session_id = uuid.uuid4()
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self.peakId = 0
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self.parameterWidget = ParameterWidget()
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self.ui.dockWidget_3.setWidget(self.parameterWidget)
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self.data = Data()
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self.fit_boundary_imag = pg.LinearRegionItem(brush=QColor(0, 127, 254, 15))
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self.fit_boundary_real = pg.LinearRegionItem(brush=QColor(0, 127, 254, 15))
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self.ui.pgPlotWidget_imag.addItem(self.data.experimental_curve_imag)
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self.ui.pgPlotWidget_real.addItem(self.data.experimental_curve_real)
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self.ui.pgPlotWidget_imag.addItem(self.data.model_curve_imag)
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self.ui.pgPlotWidget_real.addItem(self.data.model_curve_real)
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self.ui.pgPlotWidget_imag.addItem(self.fit_boundary_imag)
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self.ui.pgPlotWidget_real.addItem(self.fit_boundary_real)
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# fit boundary signals
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self.fit_boundary_imag.sigRegionChanged.connect(self._update_fit_boundary_imag)
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self.fit_boundary_imag.sigRegionChangeFinished.connect(self.update_plot)
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self.fit_boundary_real.sigRegionChanged.connect(self._update_fit_boundary_real)
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self.fit_boundary_real.sigRegionChangeFinished.connect(self.update_plot)
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for pltwidgt in (self.ui.pgPlotWidget_real, self.ui.pgPlotWidget_imag):
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pltwidgt.setLogMode(x=True, y=True)
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pltwidgt.showGrid(x=True, y=True)
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pltwidgt.disableAutoRange()
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pltwidgt.setLabel("bottom", "Frequency", units="Hz")
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self.ui.pgPlotWidget_imag.setLabel("left", u'Dielectric loss ε"', units="Debye")
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self.ui.pgPlotWidget_real.setLabel("left", u"Dielectric loss ε' ", units="Debye")
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sc_real = self.ui.pgPlotWidget_real.scene()
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sc_real.sigMouseClicked.connect(self.mousePress)
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sc_real.sigMouseMoved.connect(self.updateCrosshair)
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sc_imag = self.ui.pgPlotWidget_imag.scene()
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sc_imag.sigMouseClicked.connect(self.mousePress)
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sc_imag.sigMouseMoved.connect(self.updateCrosshair)
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self._fit_thread = QThread()
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self._fit_method = FitRoutine()
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self._fit_method.moveToThread(self._fit_thread)
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self._fit_method.finished_fit.connect(self.fitData_update)
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self._fit_method.data_ready.connect(self.updateIntermediatePlot)
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self._fit_thread.started.connect(self._fit_method.fit)
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# finally process cmd line args
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if files != []:
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self.openFile(unicode(self._file_paths[0]))
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self._current_file_index = 0
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def _init_menu( self ):
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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.getFileNames)
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fileMenu.addAction(openFile)
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nextFile = QAction("Next", self)
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nextFile.setShortcut(QKeySequence("Ctrl+k"))
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nextFile.triggered.connect(self.nextFile)
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fileMenu.addAction(nextFile)
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previousFile = QAction("Previous", self)
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previousFile.setShortcut(QKeySequence("Ctrl+j"))
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previousFile.triggered.connect(self.previousFile)
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fileMenu.addAction(previousFile)
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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("Complex NLS", 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("NLS (Imag.)", 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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self.ui.actionActionAbortFit.triggered.connect(self.abortFit)
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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_start)
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self.ui.actionShow_Derivative.triggered.connect(self.show_derivative)
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self.ui.menuConfiguration.triggered.connect(self.conf)
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def conf(self):
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pass
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def show_derivative( self ):
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self.xtra_wdgt = ExtraDifferentialWidget.DifferentialWidget()
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#self.xtra_wdgt.set
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deriv_r = np.diff(np.log10(self.data.epsilon.real))
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deriv_i = np.diff(np.log10(self.data.epsilon.imag))*0
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deriv_i = -np.pi/2*np.diff(np.log10(self.data.epsilon.real))/np.diff(np.log10(self.data.frequency))
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self.xtra_wdgt.plot(self.data.frequency[:-1], deriv_r, deriv_i)
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# self.xtra_wdgt.plot([0,1], [0,1], [0,1])
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self.xtra_wdgt.setGeometry(self.ui.pgPlotWidget_real.geometry())
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self.xtra_wdgt.show()
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#self.xtra_wdgt.showCenterd()
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self.xtra_wdgt.raise_()
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def updateCrosshair( self, evt ):
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vb_real = self.ui.pgPlotWidget_real.getPlotItem().vb
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vb_imag = self.ui.pgPlotWidget_imag.getPlotItem().vb
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if self.ui.pgPlotWidget_imag.underMouse():
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pos = vb_imag.mapSceneToView(evt)
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elif self.ui.pgPlotWidget_real.underMouse():
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pos = vb_real.mapSceneToView(evt)
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else:
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pos = QPointF(0.0, 0.0)
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self.last_pos = pos
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def mousePress( self, evt ):
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data_pos = self.last_pos
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mouse_in_imag = self.ui.pgPlotWidget_imag.underMouse()
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mouse_in_real = self.ui.pgPlotWidget_real.underMouse()
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msgBox = QMessageBox()
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if self.ui.actionAdd_Peak.isChecked():
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if mouse_in_imag:
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id_list = [key.id_num for key in
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self.function_registry.get_registered_functions()
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if key.id_string == 'hn']
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self.peakId = 1
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while self.peakId in id_list:
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self.peakId += 1
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_pk = self.addContainer(Peak, data_pos)
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_pk.set_id(self.peakId)
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# self.addPeak(data_pos)
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self.ui.actionAdd_Peak.setChecked(False)
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else:
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msgBox.setText("Click in imaginary part")
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msgBox.exec_()
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if self.ui.actionAdd_Cond.isChecked():
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if mouse_in_imag:
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self.addContainer(Conductivity, data_pos)
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self.ui.actionAdd_Cond.setChecked(False)
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else:
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msgBox.setText("Click in imaginary part")
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msgBox.exec_()
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if self.ui.actionYAFF.isChecked():
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if mouse_in_imag:
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self.addContainer(YAFF, data_pos)
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self.ui.actionYAFF.setChecked(False)
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else:
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msgBox.setText("Click in imaginary part")
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msgBox.exec_()
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if self.ui.actionAdd_PowerLaw.isChecked():
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if mouse_in_imag:
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self.addContainer(PowerComplex, data_pos)
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self.ui.actionAdd_PowerLaw.setChecked(False)
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else:
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msgBox.setText("Click in imaginary part")
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msgBox.exec_()
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if self.ui.actionAdd_Eps_Infty.isChecked():
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if mouse_in_real:
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self.addContainer(Static, data_pos)
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self.ui.actionAdd_Eps_Infty.setChecked(False)
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else:
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msgBox.setText("Click in real part")
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msgBox.exec_()
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def abortFit( self ):
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for container in self.function_registry.get_registered_functions():
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container.abort(True)
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self._fit_thread.terminate()
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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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# prepare header
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file_id = hashlib.md5(open(self._file_paths[self._current_file_index]).read()).hexdigest()
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pre_header = "# Date: {date}\n".format(date=time.strftime("%Y-%m-%d"))
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pre_header += "# Time: {time}\n# SessionID={id}\n".format(time=time.strftime("%H:%M:%S"), id=self.session_id)
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pars = []
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base_filename, file_ext = os.path.splitext(self.filepath)
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header = "{n1:13}{n2:13}".format(n1="# 0:T", n2="1:invT")
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varnum = 2 # T, invT are the first two columns
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for i_fcn, fcn in enumerate(self.function_registry.get_registered_functions()):
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fit_function_name = fcn.id_string
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for i, name in enumerate(fcn.widget.names): # get variable names
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header += "{n:13}{n_sd:13}".format(n="%i:%s"%(varnum, name), n_sd="%i:%s_sd"%(varnum+1, name))
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varnum += 2
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pre_header += "# %s\n"%fit_function_name
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# write for each function an extra file
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fit_filename = "%s_%i.fit"%(base_filename, i_fcn)
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f_fcn = open(fit_filename, 'w')
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# retrieve correct function type peak
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#if fit_function_name == "hn":
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f_fcn.write("# type=%s\n"%fcn.widget.func_type)
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f_fcn.write("# SourceID=%s\n"%file_id)
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#else:
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# f_fcn.write("# type=%s\n"%fit_function_name)
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for i, par in enumerate(fcn._beta): # params # TODO: ughh
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if fcn._selector_mask is not None:
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if fcn._selector_mask[i]:
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pars.extend([par])
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pars.extend([fcn._sd_beta[i]])
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f_fcn.write('# param=%s %e %e\n'%(fcn.widget.names[i], par, fcn._sd_beta[i]))
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else:
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pars.extend([par])
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pars.extend([fcn._sd_beta[i]])
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f_fcn.write('# param=%s %e %e\n'%(fcn.widget.names[i], par, fcn._sd_beta[i]))
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# finish writing fit function file
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f_fcn.flush()
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np.savetxt(f_fcn, fcn.resampleData(self.data.frequency))
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f_fcn.close()
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# append fit limits header
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header += "%-13s%-13s\n"%("fit_xlow", "fit_xhigh")
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# write new header if fit model changed TODO: more robust detection
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if self._last_written_header != header:
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f.write(pre_header)
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f.write(header)
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f.flush()
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self._last_written_header = header
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else:
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pass
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pars.insert(0, self.data.meta["T"])
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pars.insert(1, 1e3/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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pars = np.array([pars])
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np.savetxt(f, pars, fmt='%-12.3e', delimiter=" ")
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f.close()
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def _saveFitFigure( self ):
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fig = pyplot.figure(figsize=(3.54*1.4, 2.75*1.4))
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font = { 'family': 'sans serif',
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'weight': 'normal',
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'size': 9 }
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matplotlib.rc('font', **font)
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pyplot.grid(linestyle="solid", alpha=0.3, color="0.5")
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pyplot.loglog(self.data.frequency, self.data.epsilon.imag, 'bo', markersize=4, label="Data")
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pyplot.loglog(self.data.frequency_fit, self.data.epsilon_fit.imag, 'r-', lw=1.2, label="Fit")
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for fcn in self.function_registry.get_registered_functions():
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f, eps = fcn.get_data()
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label = fcn.id_label
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color = hex2color(str(fcn.color.name()))
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pyplot.loglog(f, eps[1], ls=":", color=color, lw=1, dashes=(1, 1), label=label)
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for i in (0, 1): pyplot.axvline(x=self.data.fit_limits[i], color='b', ls="-", lw=0.5)
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pyplot.legend(title="T=%.1f K"%(self.data.meta["T"]))
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pyplot.xlabel('f/Hz')
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pyplot.ylabel(u'ε"')
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pyplot.ylim(self.data.epsilon.imag.min(), self.data.epsilon.imag.max())
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#pyplot.savefig(os.path.splitext(self.filepath)[0]+".png")
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pyplot.savefig(os.path.splitext(self.filepath)[0]+".pdf")
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fig.clear()
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del (fig)
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def _saveFitFigureGrace( self ):
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#agrtemplate = open('template.agr').read()
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agrtemplate = """
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"""
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def addContainer(self, selected_container, pos):
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_cont = selected_container(plt_real=self.ui.pgPlotWidget_real,
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plt_imag=self.ui.pgPlotWidget_imag,
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limits=self.data.fit_limits)
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_cont.blockSignals(True)
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_cont.changedData.connect(self.update_plot)
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_cont.removeObj.connect(self.delParamterObject)
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_cont.start_parameter(pos)
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self.parameterWidget.add(_cont.widget)
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self.function_registry.register_function(_cont)
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self.update_plot()
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_cont.blockSignals(False)
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return _cont
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def delParamterObject( self, obj ):
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self.function_registry.unregister_function(obj)
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self.update_plot()
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def fitData_start( self, method ):
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#fit_methods = [fit_odr_cmplx, fit_odr_imag, fit_lbfgsb, fit_anneal]
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self.fit_boundary_real.hide()
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self.fit_boundary_imag.hide()
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fit_method = [
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self._fit_method.fit_odr_cmplx,
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self._fit_method.fit_odr_imag,
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][method]
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# build function list
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p0, funcs, fixed_params = [], [], []
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for fcn in self.function_registry.get_registered_functions():
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p0.extend(fcn.get_parameter())
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funcs.append(fcn)
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fixed_params.extend(fcn.get_fixed())
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fcn.clear_data()
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_freq, _fit = self.data.get_data()
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if not self._fit_thread.isRunning():
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#self._fit_method.fit_odr_cmplx(_freq, _fit, p0, fixed_params, funcs)
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fit_method(_freq, _fit, p0, fixed_params, funcs)
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self._fit_thread.start()
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self.ui.statusbar.showMessage("Fitting ...")
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else:
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self.ui.statusbar.showMessage("Still fitting ...")
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def fitData_update( self ):
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self._fit_thread.quit()
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odr_result = self._fit_method.result()
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p0, funcs, fixed_params = [], [], []
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for fcn in self.function_registry.get_registered_functions():
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p0.extend(fcn.get_parameter())
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funcs.append(fcn)
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fixed_params.extend(fcn.get_fixed())
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for container in self.function_registry.get_registered_functions():
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container.abort(False)
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self.data.set_fit(odr_result.beta, funcs)
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self.ui.statusbar.showMessage(" ".join(odr_result.stopreason))
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ndx = 0
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for i, fcn in enumerate(self.function_registry.get_registered_functions()):
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num_p = len(fcn.get_parameter())
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beta = odr_result.beta[ndx:num_p+ndx]
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if odr_result.sd_beta is not None:
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sd_beta = odr_result.sd_beta[ndx:num_p+ndx]
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else:
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sd_beta = None
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fcn.set_parameter(beta, sd_beta)
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ndx += num_p
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self.fit_boundary_real.show()
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self.fit_boundary_imag.show()
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def getFileNames( self ):
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tmp = QFileDialog.getOpenFileNames(self, "Open file", "", '*.dat *.TXT')
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if len(tmp) != 0:
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self._file_paths = tmp
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self._current_file_index = 0
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path = unicode(self._file_paths[self._current_file_index])
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self.openFile(path)
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def nextFile( self ):
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lim = self.fit_boundary_imag.getRegion() # store limits
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if len(self._file_paths) > self._current_file_index+1: # wrap around
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self._current_file_index += 1
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else:
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self._current_file_index = 0
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path = unicode(self._file_paths[self._current_file_index])
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self.openFile(path)
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self.fit_boundary_imag.setRegion(lim)
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def previousFile( self ):
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lim = self.fit_boundary_imag.getRegion() # store limits
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if self._current_file_index == 0: # wrap around
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self._current_file_index = len(self._file_paths)-1
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else:
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self._current_file_index -= 1
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path = unicode(self._file_paths[self._current_file_index])
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self.openFile(path)
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self.fit_boundary_imag.setRegion(lim)
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|
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def _sortInputFiles( self, files ):
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return QStringList(sorted(files, key=lambda x: re.findall("\d+\.\d+K", x)))
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|
|
|
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def openFile( self, path ):
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print "opening: %s"%path
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|
self.filepath = path
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Temp, _die_loss, _die_stor, _freq = bds_file_reader.FileReader.read_datafile(path)
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|
|
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self.setWindowTitle("%s - %.2f K"%(os.path.basename(path), Temp))
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|
|
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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_imag.setRegion([np.log10(_freq.min()), np.log10(_freq.max())])
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|
self.ui.pgPlotWidget_imag.disableAutoRange()
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|
self.ui.pgPlotWidget_real.disableAutoRange()
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|
|
|
self.ui.pgPlotWidget_imag.setXRange(np.log10(_freq.min()), np.log10(_freq.max()))
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|
self.ui.pgPlotWidget_imag.setYRange(np.log10(_die_loss.min()), np.log10(_die_loss.max()))
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|
|
|
self.ui.pgPlotWidget_real.setXRange(np.log10(_freq.min()), np.log10(_freq.max()))
|
|
self.ui.pgPlotWidget_real.setYRange(np.log10(_die_stor.min()), np.log10(_die_stor.max()))
|
|
|
|
|
|
#self.ui.pgPlotWidget_real.setRange(xRange=(_freq.min(), _freq.max()),
|
|
# yRange=(_die_stor.min(), _die_stor.max()) )
|
|
self.update_plot()
|
|
|
|
|
|
def update_plot( self ):
|
|
print "redrawing plot"
|
|
log10fmin, log10fmax = self.fit_boundary_imag.getRegion()
|
|
self.data.set_fit_xlimits(10**log10fmin, 10**log10fmax)
|
|
|
|
p0, funcs = [], []
|
|
for fcn in self.function_registry.get_registered_functions():
|
|
p0.extend(fcn.get_parameter())
|
|
funcs.append(fcn)
|
|
|
|
|
|
# calculate parametrized curve
|
|
self.data.set_fit(p0, funcs)
|
|
|
|
|
|
# replot data and fit, TODO: replot only if measurement data changed
|
|
self.data.experimental_curve_real.setData(self.data.frequency, self.data.epsilon.real)
|
|
self.data.experimental_curve_imag.setData(self.data.frequency, self.data.epsilon.imag)
|
|
#print "updatePlot: ",self.data.frequency_fit, self.data.epsilon_fit
|
|
if len(funcs) > 0:
|
|
#print "funcs > 0:",self.data.frequency_fit, self.data.epsilon_fit
|
|
self.data.model_curve_real.setData(x=self.data.frequency_fit, y=self.data.epsilon_fit.real)
|
|
self.data.model_curve_imag.setData(x=self.data.frequency_fit, y=self.data.epsilon_fit.imag)
|
|
else:
|
|
self.data.model_curve_real.setData(x=np.array([np.nan]), y=np.array([np.nan]))
|
|
self.data.model_curve_imag.setData(x=np.array([np.nan]), y=np.array([np.nan]))
|
|
|
|
|
|
def updateIntermediatePlot( self, freq, intermediate_data ):
|
|
self.data.model_curve_real.setData(freq, intermediate_data[0])
|
|
self.data.model_curve_imag.setData(freq, intermediate_data[1])
|
|
|
|
def _update_fit_boundary_imag( self ):
|
|
"""
|
|
Update real region when with imag reagion
|
|
"""
|
|
self.fit_boundary_real.setRegion(self.fit_boundary_imag.getRegion())
|
|
self._update_fit_boundary()
|
|
|
|
def _update_fit_boundary_real( self ):
|
|
"""
|
|
Update imag region when with real reagion
|
|
"""
|
|
self.fit_boundary_imag.setRegion(self.fit_boundary_real.getRegion())
|
|
self._update_fit_boundary()
|
|
|
|
def _update_fit_boundary( self ):
|
|
"""
|
|
Update limits in container.
|
|
"""
|
|
for container in self.function_registry.get_registered_functions():
|
|
lims = [10**i for i in self.fit_boundary_real.getRegion()]
|
|
container.set_limits(lims)
|
|
|
|
|
|
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.Yes) == QMessageBox.Yes:
|
|
QApplication.quit()
|
|
|
|
|
|
if __name__ == '__main__':
|
|
signal.signal(signal.SIGINT, sigint_handler)
|
|
files = sys.argv[1:]
|
|
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(files=files)
|
|
main.showMaximized()
|
|
main.raise_()
|
|
sys.exit(app.exec_())
|