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Optimized threading, bug fixes in libyaff, saveFitResult

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This commit is contained in:
Markus Rosenstihl 2014-04-11 17:30:48 +02:00
parent 78c00b701d
commit e32fa8f834
4 changed files with 115 additions and 64 deletions
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45
CustomWidgets.py
View File

@ -12,7 +12,7 @@ __author__ = 'markusro'
from PyQt4 import QtGui
from PyQt4.QtGui import *
from PyQt4.QtCore import QRegExp, pyqtSignal
from PyQt4.QtCore import QRegExp, pyqtSignal,pyqtSlot
#import PeakWidget
@ -65,6 +65,7 @@ class BaseWidget(QGroupBox):
self.inputs = []
self.errors = []
self.names = []
self.selector_mask = None # TODO: clean up
def remove(self):
self.removeMe.emit()
@ -389,9 +390,7 @@ class YaffWidget(BaseWidget):
self.ui.removeButton.clicked.connect(self.remove)
self.ui.comboBox.currentIndexChanged.connect(self.change_model)
self.change_model()
self.names = [
self._names = [
"Deps",
"tau_a",
"alpha",
@ -400,10 +399,22 @@ class YaffWidget(BaseWidget):
"tau_b",
"a",
"b",
"none",
"none"
"scale",
"g"
]
self.labels = [
self.ui.label_111,
self.ui.label_222,
self.ui.label_322,
self.ui.label_422,
self.ui.label_522,
self.ui.label_622,
self.ui.label_72,
self.ui.label_82,
self.ui.label_112,
self.ui.label_102
]
self.errors = [self.ui.label_1,
self.ui.label_2,
self.ui.label_3,
@ -442,20 +453,34 @@ class YaffWidget(BaseWidget):
for dsb in self.inputs:
dsb.valueChanged.connect(self.changeValues)
self.change_model(0)
def getYaffType(self):
return self.ui.comboBox.currentIndex()
def change_model(self):
ndx = self.ui.comboBox.currentIndex()
@pyqtSlot(int)
def change_model(self,ndx):
#ndx = self.ui.comboBox.currentIndex()
mask = [
(0,0,0,0,1,1,1,1,1,1),
(0,0,0,0,0,0,1,1,1,1),
(0,0,0,0,1,1,1,1,0,0),
(0,0,0,0,0,0,0,0,1,1),
(0,0,0,0,0,0,0,0,0,0),
]
self.names = []
for i,inp in enumerate(self.inputs):
self.inputs[i].setDisabled(mask[ndx][i])
self.inputs[i].setHidden(mask[ndx][i])
self.errors[i].setDisabled(mask[ndx][i])
self.fixedCheckBoxes[i].setDisabled(mask[ndx][i])
self.errors[i].setHidden(mask[ndx][i])
self.errors[i].setText("(---)")
self.fixedCheckBoxes[i].setChecked(mask[ndx][i])
self.fixedCheckBoxes[i].setDisabled(mask[ndx][i])
self.fixedCheckBoxes[i].setHidden(mask[ndx][i])
self.labels[i].setHidden(mask[ndx][i])
if mask[ndx][i]==0: self.names.append(self._names[i])
self.selector_mask = [not i for i in mask[ndx] ]
self.on_model_changed.emit()

68
QDS.py
View File

@ -241,9 +241,15 @@ class AppWindow(QMainWindow):
for fcn in self.function_registry.get_registered_functions():
for name in fcn.widget.names: # variable names
header += "{n:11}{n_sd:11}".format(n=name, n_sd=name+"_sd")
for i,par in enumerate(fcn._beta): # params
pars.extend([par])
pars.extend([fcn._sd_beta[i]])
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]])
else:
pars.extend([par])
pars.extend([fcn._sd_beta[i]])
header += "%-11s%-11s\n"%("fit_xlow","fit_xhigh")
@ -263,21 +269,23 @@ class AppWindow(QMainWindow):
f.close()
def saveFitFigure(self):
fig = pyplot.figure(figsize=(3.54, 2.75))
fig = pyplot.figure(figsize=(3.54*1.4, 2.75*1.4))
font = {'family' : 'sans serif',
'weight' : 'normal',
'size' : 8}
'size' : 9}
matplotlib.rc('font', **font)
pyplot.grid(linestyle="solid",alpha=0.3, color="0.5")
pyplot.loglog(self.data.frequency, self.data.epsilon.imag, 'bo', markersize=3, label="Data")
pyplot.loglog(self.data.frequency, self.data.epsilon.imag, 'bo', markersize=4, label="Data")
pyplot.loglog(self.data.frequency_fit, self.data.epsilon_fit.imag, 'r-', lw=1.2, label="Fit")
for fcn in self.function_registry.get_registered_functions():
f,eps = fcn.get_data()
pyplot.loglog(f,eps[1], ls=":", color=hex2color(str(fcn.color.name())) , lw=1, dashes=(1,2))
label = fcn.id_string
color = hex2color(str(fcn.color.name()))
pyplot.loglog(f,eps[1], ls=":", color=color, lw=1, dashes=(1,1), label=label)
for i in (0,1): pyplot.axvline(x=self.data.fit_limits[i], color='b', ls="-", lw=0.5)
pyplot.legend(title = "T=%.1f K"%(self.data.meta["T"]))
@ -297,8 +305,8 @@ class AppWindow(QMainWindow):
_yaff.blockSignals(True)
_yaff.changedData.connect(self.updatePlot)
_yaff.removeObj.connect(self.delParamterObject)
gg_y = 10**pos.y()
gg_x = 10**pos.x()*2*np.pi
gg_y = 10**pos.y()*2
gg_x = 1/(10**pos.x()*2*np.pi)
yaff_par = [ gg_y, gg_x , 20.0, 1.0, 0.5, gg_x/100, 1.0, 1.0]
_yaff.setParameter(beta=yaff_par)
self.parameterWidget.add(_yaff.widget)
@ -405,32 +413,38 @@ class AppWindow(QMainWindow):
p0,funcs,fixed_params = [],[],[]
for fcn in self.function_registry.get_registered_functions():
p0.extend(fcn.getParameter())
#funcs.append(fcn.id_string)
funcs.append(fcn)
fixed_params.extend(fcn.getFixed())
fcn.clearData()
_freq, _fit = self.data.get_data()
# Prepare
self._fit_method = FitRoutine()
self._fit_method.moveToThread(self._fit_thread)
self._fit_method.finished_fit.connect(self.fitData_update)
self._fit_method.fit_odr_cmplx(_freq, _fit, p0, fixed_params, funcs)
self._fit_method.data_ready.connect(self.updateIntermediatePlot)
self._fit_thread.started.connect(self._fit_method.fit)
self._fit_thread.start()
self.ui.statusbar.showMessage("Fitting ...")
if not self._fit_thread.isRunning():
self._fit_method = FitRoutine()
self._fit_method.moveToThread(self._fit_thread)
self._fit_method.finished_fit.connect(self.fitData_update)
self._fit_method.fit_odr_cmplx(_freq, _fit, p0, fixed_params, funcs)
self._fit_method.data_ready.connect(self.updateIntermediatePlot)
#for fun in funcs:
# self._fit_method.data_ready.connect(fun.updateData)
self._fit_thread.started.connect(self._fit_method.fit)
self._fit_thread.finished.connect(self._fit_method.deleteLater)
self._fit_thread.start()
self.ui.statusbar.showMessage("Fitting ...")
else:
print "fit is still running"
pass
def fitData_update(self):
self._fit_thread.quit()
odr_result = self._fit_method.result()
print "before thread.quit"
print "running thread?:",self._fit_thread.isRunning()
self._fit_thread.quit()
print "after thread.quit"
print "running thread?:",self._fit_thread.isRunning()
odr_result = self._fit_method.result()
print odr_result
# build function list
p0,funcs,fixed_params = [],[],[]
for fcn in self.function_registry.get_registered_functions():

24
data.py
View File

@ -1,3 +1,4 @@
# -*- encoding: utf8 -*-
from PyQt4.QtGui import QColor
import numpy as np
import pyqtgraph as pg
@ -98,6 +99,7 @@ class BaseObject(QObject):
self._func = None
self._beta = None
self._sd_beta = None
self._selector_mask = None
self._param_number = 0
@property
@ -114,7 +116,8 @@ class BaseObject(QObject):
@id_string.setter
def id_string(self, id):
self._func = self.functions.get_function(id)
#self._func = self.functions.get_function(id)
self._func = self.function
self._id = id
@property
@ -166,6 +169,10 @@ class BaseObject(QObject):
self.data_curve_imag.setData(x=self._frequency, y=self._data[1])
self.changedData.emit()
def clearData(self):
self.data_curve_real.setData(x=[np.nan], y=[np.nan])
self.data_curve_imag.setData(x=[np.nan], y=[np.nan])
def function(self,p,x):
raise NotImplementedError, "This needs to be implemented in your subclass"
@ -174,7 +181,7 @@ class Conductivity(BaseObject):
super(Conductivity, self).__init__(plt_real=plt_real, plt_imag=plt_imag, limits=limits)
self.widget = CustomWidgets.ConductivityWidget()
self.color = QColor("blue")
self.id_string = "conductivity"
self.id_string = "Cond."
self.param_number = 3
@ -191,7 +198,7 @@ class PowerComplex(BaseObject):
super(PowerComplex, self).__init__(plt_real=plt_real, plt_imag=plt_imag, limits=limits)
self.widget = CustomWidgets.PowerLawWidget()
self.color = QColor("#ff44c4")
self.id_string = 'power'
self.id_string = 'Power Law'
self.param_number = 2
def function( self, p, x ):
@ -207,7 +214,7 @@ class Static(BaseObject):
super(Static, self).__init__(plt_real=plt_real, plt_imag=plt_imag, limits=limits)
self.widget = CustomWidgets.StaticWidget()
self.color = QColor('#FF0F13')
self.id_string = 'static'
self.id_string = u'ε(∞)'
self.param_number = 1
def function( self, p, x ):
@ -240,10 +247,11 @@ class YAFF(BaseObject):
super(YAFF, self).__init__(plt_real=plt_real, plt_imag=plt_imag, limits=limits)
self.widget = CustomWidgets.YaffWidget()
self.widget.on_model_changed.connect(self.change_model)
self.id_string = "yaff"
self.color = QColor(32, 120, 29, int(255*0.82))
self._libyaff = libyaff.Yaff(self.widget.getYaffType())
self.id_string = self._libyaff.label
self._param_number = self._libyaff.params
self._selector_mask = self.widget.selector_mask
@property
def param_number(self):
@ -255,12 +263,14 @@ class YAFF(BaseObject):
def change_model(self):
self._libyaff = libyaff.Yaff(self.widget.getYaffType())
self._selector_mask = self.widget.selector_mask
self.id_string = self._libyaff.label
self.param_number = self._libyaff.params
self.updateData()
def function( self, p, x ):
ya = self._libyaff.loss( p[:self.param_number], x)
ya = self._libyaff.loss( p, x)
cplx = np.array([ya.imag, ya.real])
return cplx

42
libyaff.py
View File

@ -26,10 +26,12 @@ class PhiT:
def __init__(self, dist_x, dist_y):
self.dist_x = dist_x
self.dist_y = dist_y
def __call__(self,t):
kern = self.dist_y*exp(-t/self.dist_x)
phi = scipy.integrate.simps(kern,log(self.dist_x))
return phi
def __call__(self, ts):
phis = zeros(ts.size)
for i,t in enumerate(ts):
kern = self.dist_y*exp(-t/self.dist_x)
phis[i] = scipy.integrate.simps(kern, log(self.dist_x))
return phis
class Yaff(QObject):
@ -39,14 +41,13 @@ class Yaff(QObject):
self.dist_x = logspace(-10,5,512)
self.dist_y = zeros(self.dist_x.size)
yaff = [
(self.yaff_gg, 4),
(self.yaff_gge, 6),
(self.yaff, 8),
(self.yaff_extended, 10),
(self.yaff_gg, "GG"),
(self.yaff_gge, "GGe"),
(self.yaff, "GG + GGb"),
(self.yaff_extended, "GGe + GGb"),
]
self.loss, self.params = yaff[dist_type]
self.loss, self.label = yaff[dist_type]
self.params = 10
def gg(self, p, tau):
tau0, a, b = p
"""
@ -64,7 +65,7 @@ class Yaff(QObject):
return norm_ggb*g
def gg_hw(self, p ,tau):
tau0, a, b, g, s = p
tau0, a, b, s,g = p
"""
Generalized Gamma function with HF wing.
s gives the onset of the wing in units of tau0, i.e. 100 means 100*tau0 or two decades later
@ -83,22 +84,23 @@ class Yaff(QObject):
epp[i] += 1j*scipy.integrate.simps(kern_imag,log(dist_x))
return epp
# serial version
def dist_to_relax_(self, ts,dist_x,dist_y):
phi = zeros(len(ts))
for i,t in enumerate(ts):
phi[i] = self.phi_t(t,dist_x,dist_y)
return phi
# parallel version
def dist_to_relax(self, ts,dist_x,dist_y):
phi = zeros(len(ts))
pool = multiprocessing.Pool()
result = pool.map(PhiT(dist_x,dist_y), ts)
num_cpus = multiprocessing.cpu_count()
ts_chunks = array_split(ts,num_cpus)
result = pool.map(PhiT(dist_x,dist_y), ts_chunks )
pool.close()
pool.terminate()
pool.join()
return array(result)
return concatenate(result)
def phi_t(self, t, dist_x, dist_y):
@ -157,7 +159,7 @@ class Yaff(QObject):
"""
GG + GB
"""
delta_eps, tau1, a1, b1, lambd, tau2, a2, b2 = p
delta_eps, tau1, a1, b1, lambd, tau2, a2, b2, s, g = p
dist_ggb = self.ggb(p=[tau2,a2,b2], tau=self.dist_x)
dist_gg = self.gg (p=[tau1,a1,b1], tau=self.dist_x)
@ -182,7 +184,7 @@ class Yaff(QObject):
"""
GG
"""
delta_eps, tau1,a1,b1 = p
delta_eps, tau1, a1, b1, lambd, tau2, a2, b2, s, g = p
ts = logspace(-10,5,512)
dist_gg = self.gg(p=[tau1,a1,b1], tau=self.dist_x)
self.dist_y = dist_gg
@ -195,7 +197,7 @@ class Yaff(QObject):
"""
GG
"""
delta_eps, tau1, a1, b1, s, g = p
delta_eps, tau1, a1, b1, lambd, tau2, a2, b2, s, g = p
ts = logspace(-10,5,512)
dist_gg = self.gg_hw(p=[tau1, a1, b1, s, g], tau=self.dist_x)
self.dist_y = dist_gg