Preliminary gracedriver works, coloring of the peaks fixed, result output: peaks ordered by tau value
This commit is contained in:
parent
30ded06b95
commit
fcee731d35
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@ -12,16 +12,18 @@ import libyaff
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def id_to_color( id ):
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colors = [
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QColor(54, 22, 115),
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QColor(160, 16, 36),
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QColor(45, 142, 15),
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QColor(255, 255, 255),
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QColor(168, 149, 17),
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QColor(45, 142, 15),
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QColor(160, 16, 36),
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QColor(54, 22, 115),
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QColor(36, 10, 85),
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QColor(118, 8, 23),
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QColor(31, 105, 7),
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QColor(124, 109, 8),
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]
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return colors[id%len(colors)]
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chosen_color = colors[id%len(colors)]
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return chosen_color
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class FitFunctionCreator(QObject):
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@ -2,8 +2,8 @@
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# Form implementation generated from reading ui file 'ConductivityGroupBox.ui'
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#
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# Created: Tue Jul 29 08:56:48 2014
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# by: PyQt4 UI code generator 4.11.1
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# Created: Tue Sep 23 21:38:12 2014
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# by: PyQt4 UI code generator 4.11.1
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#
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# WARNING! All changes made in this file will be lost!
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@ -12,21 +12,19 @@ from PyQt4 import QtCore, QtGui
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try:
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_fromUtf8 = QtCore.QString.fromUtf8
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except AttributeError:
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def _fromUtf8( s ):
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def _fromUtf8(s):
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return s
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try:
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_encoding = QtGui.QApplication.UnicodeUTF8
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def _translate( context, text, disambig ):
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def _translate(context, text, disambig):
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return QtGui.QApplication.translate(context, text, disambig, _encoding)
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except AttributeError:
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def _translate( context, text, disambig ):
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def _translate(context, text, disambig):
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return QtGui.QApplication.translate(context, text, disambig)
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class Ui_ConductivityGroupBox(object):
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def setupUi( self, ConductivityGroupBox ):
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def setupUi(self, ConductivityGroupBox):
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ConductivityGroupBox.setObjectName(_fromUtf8("ConductivityGroupBox"))
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ConductivityGroupBox.resize(253, 156)
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sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Preferred, QtGui.QSizePolicy.Preferred)
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@ -63,7 +61,7 @@ class Ui_ConductivityGroupBox(object):
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self.checkBox_3.setText(_fromUtf8(""))
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self.checkBox_3.setChecked(True)
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self.checkBox_3.setObjectName(_fromUtf8("checkBox_3"))
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self.gridLayout.addWidget(self.checkBox_3, 3, 3, 1, 1, QtCore.Qt.AlignHCenter | QtCore.Qt.AlignVCenter)
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self.gridLayout.addWidget(self.checkBox_3, 3, 3, 1, 1, QtCore.Qt.AlignHCenter|QtCore.Qt.AlignVCenter)
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self.label_2 = QtGui.QLabel(ConductivityGroupBox)
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sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Minimum, QtGui.QSizePolicy.Preferred)
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sizePolicy.setHorizontalStretch(0)
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@ -137,25 +135,18 @@ class Ui_ConductivityGroupBox(object):
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QtCore.QObject.connect(self.removeButton, QtCore.SIGNAL(_fromUtf8("clicked()")), ConductivityGroupBox.hide)
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QtCore.QMetaObject.connectSlotsByName(ConductivityGroupBox)
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def retranslateUi( self, ConductivityGroupBox ):
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def retranslateUi(self, ConductivityGroupBox):
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ConductivityGroupBox.setWindowTitle(_translate("ConductivityGroupBox", "GroupBox", None))
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ConductivityGroupBox.setTitle(_translate("ConductivityGroupBox", "Conductivity", None))
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self.pwrSigma_sd.setText(_translate("ConductivityGroupBox", "TextLabel", None))
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self.label_2.setText(_translate("ConductivityGroupBox",
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"<html><head/><body><p>σ\'<span style=\" vertical-align:sub;\">(DC)</span></p></body></html>",
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None))
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self.label_2.setText(_translate("ConductivityGroupBox", "<html><head/><body><p>σ\'<span style=\" vertical-align:sub;\">(DC)</span></p></body></html>", None))
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self.label.setText(_translate("ConductivityGroupBox", "Fix", None))
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self.removeButton.setText(_translate("ConductivityGroupBox", "Remove", None))
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self.label_4.setText(_translate("ConductivityGroupBox", "α", None))
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self.rSigma_sd.setText(_translate("ConductivityGroupBox", "TextLabel", None))
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self.rSigma.setToolTip(_translate("ConductivityGroupBox",
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"<html><head/><body><p>DC conductivity, should only be seen in the imaginary permitivity. If there is a Jonscher type of U<span style=\" font-style:italic;\">niversal Dielectric Response, </span>the ratio of σ"/σ\'<span style=\" vertical-align:sub;\">(DC)</span> is a constant</p></body></html>",
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None))
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self.rSigma.setToolTip(_translate("ConductivityGroupBox", "<html><head/><body><p>DC conductivity, should only be seen in the imaginary permitivity. If there is a Jonscher type of U<span style=\" font-style:italic;\">niversal Dielectric Response, </span>the ratio of σ"/σ\'<span style=\" vertical-align:sub;\">(DC)</span> is a constant</p></body></html>", None))
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self.subtractConductivityButton.setText(_translate("ConductivityGroupBox", "Hide", None))
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self.label_3.setText(
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_translate("ConductivityGroupBox", "<html><head/><body><p>σ"</p></body></html>", None))
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self.iSigma.setToolTip(_translate("ConductivityGroupBox",
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"<html><head/><body><p>If there is a Jonscher type of U<span style=\" font-style:italic;\">niversal Dielectric Response, </span>the ratio of σ"/σ\'<span style=\" vertical-align:sub;\">(DC)</span> is a constant</p></body></html>",
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None))
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self.label_3.setText(_translate("ConductivityGroupBox", "<html><head/><body><p>σ"</p></body></html>", None))
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self.iSigma.setToolTip(_translate("ConductivityGroupBox", "<html><head/><body><p>If there is a Jonscher type of U<span style=\" font-style:italic;\">niversal Dielectric Response, </span>the ratio of σ"/σ\'<span style=\" vertical-align:sub;\">(DC)</span> is a constant</p></body></html>", None))
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self.iSigma_sd.setText(_translate("ConductivityGroupBox", "TextLabel", None))
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12
Container.py
12
Container.py
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@ -32,7 +32,6 @@ class BaseObject(QObject):
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self.limits = limits
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# private varaibles
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#self.functions = Functions()
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self._color = QColor("white")
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self._id_label = None
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@ -47,6 +46,10 @@ class BaseObject(QObject):
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self._param_number = 0
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self._abort = False
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def set_limits(self, limits):
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self.limits = limits
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self.updateData()
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@pyqtSlot(bool)
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def abort(self, abort=False):
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self._abort = abort
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@ -86,8 +89,9 @@ class BaseObject(QObject):
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@color.setter
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def color(self, c):
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self._color = c
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self.data_curve_real.setPen(c)
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self.data_curve_imag.setPen(c)
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print c
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self.data_curve_real.setPen(color=c, style=Qt.DotLine, width=2.5)
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self.data_curve_imag.setPen(color=c, style=Qt.DotLine, width=2.5)
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@property
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def widget(self):
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@ -124,6 +128,7 @@ class BaseObject(QObject):
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self.changedData.emit()
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def updateData(self):
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self._frequency = np.logspace(np.log10(self.limits[0]), np.log10(self.limits[1]), 256)
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self._data = self._func(self.getParameter(), self._frequency)
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self.data_curve_real.setData(x=self._frequency, y=self._data[0])
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self.data_curve_imag.setData(x=self._frequency, y=self._data[1])
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@ -190,7 +195,6 @@ class Static(BaseObject):
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def function( self, p, x ):
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BaseObject.function(self,p,x)
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eps_inf = p[0]
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static = np.ones( (2,x.size) )*eps_inf
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static[1,:] *= 0 # set imag part zero
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@ -63,6 +63,7 @@ class BaseWidget(QGroupBox):
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self.errors = []
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self.names = []
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self.selector_mask = None # TODO: clean up
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self.func_type="None"
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def remove(self):
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self.removeMe.emit()
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@ -149,6 +150,8 @@ class PeakWidget(BaseWidget,QGroupBox):
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"beta"
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]
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self.func_type="HN"
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self.inputs = [
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self.ui.doubleSpinBox_1,
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self.ui.doubleSpinBox_2,
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@ -163,9 +166,6 @@ class PeakWidget(BaseWidget,QGroupBox):
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self.ui.label_8,
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]
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for dsb in self.inputs:
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dsb.valueChanged.connect(self.changeValues)
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@ -183,7 +183,7 @@ class PeakWidget(BaseWidget,QGroupBox):
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self.ui.checkBox_3.setChecked(False)
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self.ui.checkBox_3.setDisabled(False)
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self.ui.checkBox_4.setChecked(False)
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self.ui.checkBox_3.setDisabled(False)
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self.ui.checkBox_4.setDisabled(False)
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self.ui.doubleSpinBox_3.setDisabled(False)
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self.ui.doubleSpinBox_4.setDisabled(False)
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@ -202,8 +202,10 @@ class PeakWidget(BaseWidget,QGroupBox):
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self.ui.checkBox_3.setChecked(True)
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self.ui.checkBox_3.setDisabled(True)
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self.ui.checkBox_4.setChecked(False)
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self.func_type = "CD"
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else:
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self.ui.doubleSpinBox_3.setDisabled(False)
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self.func_type = "HN"
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def _distrib_debye(self, state):
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if state:
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@ -215,10 +217,12 @@ class PeakWidget(BaseWidget,QGroupBox):
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self.ui.checkBox_3.setDisabled(True)
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self.ui.checkBox_4.setChecked(True)
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self.ui.checkBox_4.setDisabled(True)
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self.func_type = "Debye"
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else:
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self.ui.doubleSpinBox_3.setDisabled(False)
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self.ui.doubleSpinBox_4.setDisabled(False)
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self.func_type = "HN"
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def _distrib_cc(self, state):
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@ -229,8 +233,12 @@ class PeakWidget(BaseWidget,QGroupBox):
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self.ui.checkBox_3.setChecked(False)
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self.ui.checkBox_4.setChecked(True)
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self.ui.checkBox_4.setDisabled(True)
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self.func_type = "CC"
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else:
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self.ui.doubleSpinBox_4.setDisabled(False)
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self.func_type = "HN"
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def setId(self, id):
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@ -291,6 +299,7 @@ class StaticWidget(BaseWidget, QGroupBox):
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dsb.valueChanged.connect(self.changeValues)
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self.ui.removeButton.clicked.connect(self.remove)
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self.func_type=r"$\epsilon_\infty$"
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@ -314,11 +323,12 @@ class ConductivityWidget(BaseWidget, QGroupBox):
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self.ui.removeButton.clicked.connect(self.remove)
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#self.ui.subtractConductivityButton.connect(self.subtract)
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self.func_type="Cond."
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self.names = [
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"iSigma",
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"rSigma",
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"pwrSigma",
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"iSig",
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"rSig",
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"pwrSig",
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]
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self.errors = [self.ui.iSigma_sd,
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self.ui.rSigma_sd,
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@ -350,6 +360,7 @@ class PowerLawWidget(BaseWidget):
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self.ui.doubleSpinBox_2 = LogFSpinBox(self)
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self.ui.gridLayout.addWidget(self.ui.doubleSpinBox_2,1,1)
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self.ui.removeButton.clicked.connect(self.remove)
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self.func_type="Power Law"
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self.names = ["Amp", "pwrAmp"]
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self.errors = [self.ui.label_5,
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@ -371,8 +382,10 @@ class YaffWidget(BaseWidget):
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def __init__(self, parent=None):
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#QGroupBox.__init__(self)
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BaseWidget.__init__(self)
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super(YaffWidget, self).__init__(parent)
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self.func_type="YAFF" # Todo wie bei peak für gg gb gge etc.
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self.ui = YAFFparameters.Ui_Form()
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self.ui.setupUi(self)
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self.ui.doubleSpinBox_1.setParent(None)
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@ -473,11 +486,13 @@ class YaffWidget(BaseWidget):
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@pyqtSlot(int)
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def change_model(self,ndx):
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#ndx = self.ui.comboBox.currentIndex()
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mask = [
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(0,0,0,0,1,1,1,1,1,1),
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(0,0,0,0,1,1,1,1,0,0),
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(0,0,0,0,0,0,0,0,1,1),
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(0,0,0,0,0,0,0,0,0,0),
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mask = [ # 0 show, 1 hide
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(0,0,0,0,1,1,1,1,1,1), # GG
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(0,0,0,0,1,1,1,1,0,0), # GGe
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(0,1,1,1,1,0,0,0,1,1), # Gb
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(0,0,0,0,0,0,0,0,1,1), # GG + Gb
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(0,0,0,0,0,0,0,0,0,0), # GGe + Gb
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]
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self.names = []
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110
QDS.py
110
QDS.py
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@ -2,10 +2,13 @@
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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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@ -15,7 +18,6 @@ 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 time
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import pyqtgraph as pg
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from Container import Conductivity, PowerComplex, Static, Peak, YAFF
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@ -48,7 +50,7 @@ class AppWindow(QMainWindow):
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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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@ -68,8 +70,11 @@ class AppWindow(QMainWindow):
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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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self.fit_boundary_imag.sigRegionChanged.connect(self._update_fit_boundary)
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self.fit_boundary_real.sigRegionChanged.connect(self._update_fit_boundary)
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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.updatePlot)
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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.updatePlot)
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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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@ -240,40 +245,86 @@ class AppWindow(QMainWindow):
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else:
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f = open("fitresults.log", "a")
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# prepare header
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header = "# Date: {date}\n".format(date=time.ctime())
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header += "{n1:13}{n2:13}".format(n1="# 0:T", n2="1:invT")
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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 = os.path.splitext(self.filepath)[0]
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base_filename, file_ext = os.path.splitext(self.filepath)
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# print "Registered Functions (saveFitResult): ",self.function_registry.get_registered_functions()
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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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# sort peaks by time constant tau
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sorted_functions = list()
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tau_comp = 0
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for i_fcn, fcn in enumerate(self.function_registry.get_registered_functions()):
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if fcn.id_string == "hn":
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for i,varname in enumerate(fcn.widget.names):
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if varname == "tau":
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if fcn._beta[i] <= tau_comp:
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sorted_functions.append(fcn)
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else:
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sorted_functions.insert(0,fcn)
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tau_comp = fcn._beta[i]
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# eps_infty to the front
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for a in self.function_registry.get_registered_functions():
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print a.id_string
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if a.id_string == "eps_infty":
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sorted_functions.insert(0,a)
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print a
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# sort the rest lexigraphically
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for a in self.function_registry.get_registered_functions():
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if a.id_string == "pwr":
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sorted_functions.append(a)
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print a
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for a in self.function_registry.get_registered_functions():
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if a.id_string == "cond":
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sorted_functions.append(a)
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print a
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for a in self.function_registry.get_registered_functions():
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if a.id_string == "yaff":
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print a
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sorted_functions.append(a)
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print sorted_functions
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for i_fcn, fcn in enumerate(sorted_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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# write for each function extra file
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# write for each function an extra file
|
||||
fit_filename = "%s_%i.fit"%(base_filename, i_fcn)
|
||||
f_fcn = open(fit_filename, 'w')
|
||||
f_fcn.write("# %s\n"%fit_function_name)
|
||||
f_fcn.flush()
|
||||
np.savetxt(f_fcn, fcn.resampleData(self.data.frequency))
|
||||
f_fcn.close()
|
||||
# retrieve correct function type peak
|
||||
#if fit_function_name == "hn":
|
||||
f_fcn.write("# type=%s\n"%fcn.widget.func_type)
|
||||
f_fcn.write("# SourceID=%s\n"%file_id)
|
||||
#else:
|
||||
# f_fcn.write("# type=%s\n"%fit_function_name)
|
||||
for i,par in enumerate(fcn._beta): # params # TODO: ughh
|
||||
if fcn._selector_mask is not None:
|
||||
if fcn._selector_mask[i]:
|
||||
pars.extend([par])
|
||||
pars.extend([fcn._sd_beta[i]])
|
||||
f_fcn.write('# param=%s %e %e\n'%(fcn.widget.names[i], par, fcn._sd_beta[i]))
|
||||
else:
|
||||
pars.extend([par])
|
||||
pars.extend([fcn._sd_beta[i]])
|
||||
f_fcn.write('# param=%s %e %e\n'%(fcn.widget.names[i], par, fcn._sd_beta[i]))
|
||||
|
||||
# finish writing fit function file
|
||||
f_fcn.flush()
|
||||
np.savetxt(f_fcn, fcn.resampleData(self.data.frequency))
|
||||
f_fcn.close()
|
||||
|
||||
# append fit limits header
|
||||
header += "%-13s%-13s\n"%("fit_xlow", "fit_xhigh")
|
||||
|
||||
# write new header if fit model changed
|
||||
# write new header if fit model changed TODO: more robust detection
|
||||
if self._last_written_header != header:
|
||||
f.write(pre_header)
|
||||
f.write(header)
|
||||
f.flush()
|
||||
self._last_written_header = header
|
||||
|
|
@ -387,9 +438,12 @@ class AppWindow(QMainWindow):
|
|||
|
||||
def addPeak(self, pos):
|
||||
id_list = [ key.id_num for key in
|
||||
self.function_registry.get_registered_functions().keys()
|
||||
if key.id_label == 'hn']
|
||||
self.function_registry.get_registered_functions()
|
||||
if key.id_string == 'hn']
|
||||
for k in self.function_registry.get_registered_functions():
|
||||
print k.id_num,k.id_label
|
||||
self.peakId = 1
|
||||
print id_list
|
||||
while self.peakId in id_list:
|
||||
self.peakId += 1
|
||||
_peak = Peak(id_num=self.peakId,
|
||||
|
|
@ -549,9 +603,12 @@ class AppWindow(QMainWindow):
|
|||
for fcn in self.function_registry.get_registered_functions():
|
||||
p0.extend(fcn.getParameter())
|
||||
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.data_curve_real.setData(self.data.frequency, self.data.epsilon.real)
|
||||
self.data.data_curve_imag.setData(self.data.frequency, self.data.epsilon.imag)
|
||||
|
|
@ -569,10 +626,27 @@ class AppWindow(QMainWindow):
|
|||
self.data.fitted_curve_real.setData(freq, intermediate_data[0])
|
||||
self.data.fitted_curve_imag.setData(freq, intermediate_data[1])
|
||||
|
||||
def _update_fit_boundary( self ):
|
||||
def _update_fit_boundary_imag( self ):
|
||||
"""
|
||||
Update real region when with imag reagion
|
||||
"""
|
||||
self.fit_boundary_real.setRegion(self.fit_boundary_imag.getRegion())
|
||||
self.fit_boundary_imag.setRegion(self.fit_boundary_real.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):
|
||||
"""
|
||||
|
|
|
|||
|
|
@ -28,10 +28,9 @@ class grace:
|
|||
np.savetxt(tmp_name, np.array([x, y]).T)
|
||||
#tmp_fd.close()
|
||||
self.cmds.append('READ NXY "%s"\n'%tmp_name)
|
||||
self.cmds.append('S%i SYMBOL SIZE 0.6\n'%(self.data_counter))
|
||||
self.cmds.append('S%i SYMBOL SIZE 0.7\n'%(self.data_counter))
|
||||
self.cmds.append('S%i SYMBOL COLOR 1\n'%(self.data_counter))
|
||||
|
||||
|
||||
#self.cmds.append('S%i SYMBOL FILL COLOR %i\n'%(self.data_counter, self.data_counter))
|
||||
self.cmds.append('S%i SYMBOL FILL PATTERN 1\n'%(self.data_counter))
|
||||
self.cmds.append('S%i SYMBOL 1\n'%(self.data_counter)) # No line
|
||||
|
||||
|
|
@ -49,6 +48,8 @@ class grace:
|
|||
sym = kwds["sym"]
|
||||
if sym in self.sym_map.keys():
|
||||
self.cmds.append('S%i SYMBOL %i\n'%(self.data_counter, self.sym_map[sym]))
|
||||
if sym in ['+', 'x', '*']:
|
||||
self.cmds.append('S%i SYMBOL COLOR %i\n'%(self.data_counter, self.data_counter))
|
||||
else:
|
||||
print "Symbol not known: %s"%sym
|
||||
|
||||
|
|
@ -93,16 +94,20 @@ class grace:
|
|||
|
||||
if __name__ == "__main__":
|
||||
print "Testing Grace driver"
|
||||
nums = 50
|
||||
np.random.seed(1337) # make it reproducible
|
||||
nums = 30
|
||||
gr = grace()
|
||||
for i in xrange(20):
|
||||
gr.plot(np.arange(nums), np.random.random(nums), label="label %i"%i,
|
||||
t = np.linspace(0,1,nums)
|
||||
for i in xrange(30):
|
||||
gr.plot(t, i + np.sin(2*np.pi * 3 * t + i*0.33 ) + 0.3*np.random.random(nums),
|
||||
label="label %i"%i,
|
||||
ls=gr.ls_map.keys()[i%(len(gr.ls_map))],
|
||||
sym=gr.sym_map.keys()[i%(len(gr.sym_map))],
|
||||
)
|
||||
gr.xlabel(r"xlabel / \xm\sl\N\0")
|
||||
gr.ylabel(r"ylabel / \xt\sS\N\0")
|
||||
gr.save("test.agr")
|
||||
print "created test.agr"
|
||||
os.system("xmgrace test.agr")
|
||||
print "deleting test.agr"
|
||||
os.remove("test.agr")
|
||||
Loading…
Reference in New Issue
Block a user