/
angular_distr.py
460 lines (407 loc) · 14.7 KB
/
angular_distr.py
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"""
Requirements:
Python v2.7 or later (not compatible with Python 3)
numpy, matplotlib, scipy
Tested with:
Linux Mint 14 64bit
python 2.7.3
numpy 1.6.2
matplotlib 1.2.1
scipy 0.10.1
Version History:
"""
from __future__ import division
from lmfit import *
from helper import SemiPolarPlot
from numpy import arange, cos, radians, max, min, array, linspace, pi
from sys import stderr
from scipy.integrate import quad
class AngularDistribution(object):
def __init__(self, REMPISetups, Integrals, ICE=None,
fit=True, plot=True,
Normalized=True, exclude=[]):
if len(REMPISetups) != len(Integrals):
stderr.write('Error: Dimensions of Setups and ' +
'Integrals do not match!')
return
self.__ICE = ICE
self.__Setups = REMPISetups
self.__Normalized = Normalized
self.__Angles = array([setup.Angle for setup in self.__Setups])
self.__excluded = []
if ICE != None:
for i in range(len(Integrals)):
Integrals[i] = Integrals[i]/ICE(self.__Setups[i].ZR)
self.__Integrals = array(Integrals)
self.__NormIntegrals = self.__norm(Integrals)
self.__fit = None
if fit:
self.fit(verbose=False, plot=False, exclude=exclude)
if plot:
self.plot()
def testfunc(self, theta, A, m, theta0):
return A * cos(radians(theta-theta0))**m
def fit(self, func=None, p0={'A':1, 'theta0': 3, 'm': 3}, verbose=True,
plot=False, exclude=[], Normalized=True):
self.__Normalized = Normalized
self.__excluded = exclude
if func == None:
func = self.testfunc
if Normalized:
Integrals = self.__NormIntegrals
else:
Integrals = self.__Integrals
ex = set(exclude)
idx = set(range(len(Integrals)))
idx = list(idx.difference(ex))
Integrals = Integrals[idx]
Angles = self.__Angles[idx]
self.__fit = lmfit(func, Angles, Integrals, p0, verbose=verbose,
plot=plot)
def plot(self):
if self.__Normalized:
y = self.__NormIntegrals
else:
y = self.__Integrals
fig = plt.figure(1, figsize=(8, 8))
fig.clf()
ax1, polar_ax = SemiPolarPlot(fig)
exclude = self.__excluded
idx = list(set(range(len(y))).difference(set(exclude)))
polar_ax.plot(self.__Angles[idx], y[idx], 'bo',
label=r'$\mathrm{Experimental\ Data}$')
theta = linspace(-90, 90, 300)
if self.__fit is not None:
label = r'$%1.2f\ \cos^{%2.1f}(\theta-%1.2f^\circ)$' %\
(self.Fit.P['A'], self.Fit.P['m'], self.Fit.P['theta0'])
polar_ax.plot(theta, self.Fit(theta), 'b-', label=label)
label = r'$\cos(\theta)$' % self.Fit.P['theta0']
polar_ax.plot(theta, cos(radians(theta)),
'k--', label=label)
if len(self.__excluded) > 0:
polar_ax.plot(self.__Angles[self.__excluded],
y[self.__excluded], 'ro',
label=r'$\mathrm{Excluded\ Data\ Points}$')
ax1.legend(loc='best', numpoints=1)
ax1.set_title(r"""Angular Distribution""")
self.fig = fig
self.axis1 = ax1
self.polar_axis = polar_ax
self.savefig = fig.savefig
plt.show(fig)
def __norm(self, x):
return x/max(x)
def __call__(self, theta):
return self.__fit(theta)
@property
def Integral(self):
b = self.Fit.P['theta0']
return quad(self, -90+b, 90+b)[0]
@property
def FitParams(self):
return self.Fit.P['m'], self.Fit.P['theta0']
@property
def Angles(self):
return self.__Angles
@property
def Setups(self):
return self.__Setups
@property
def Integrals(self):
return self.__Integrals
@property
def NormIntegrals(self):
return self.__NormIntegrals
@property
def Fit(self):
return self.__fit
from matplotlib.path import Path
import matplotlib.patches as patches
from numpy import arctan, sqrt, degrees
import matplotlib.pylab as plt
import matplotlib.gridspec as gs
class REMPISetup(object):
def __init__(self, SurfacePosMeas,
Positions={'REMPI': 0, 'Center ZRM': 5.1, 'ZRM': 3.5,
'ZRM Beam Offset': 4.6, 'Surface Y': None},
visualize=False):
self.__SurfacePosMeas = SurfacePosMeas
self.__Pos = Positions
self.__l, self.__angle = self.calc(Positions)
if visualize == True:
self.visualize()
# PUBLIC ATTRIBUTES
@property
def ZR(self):
return self.__Pos['Center ZRM'] - self.__Pos['ZRM']
@property
def Positions(self):
return self.__Pos
@property
def SurfacePosMeas(self):
return self.__SurfacePosMeas
@property
def FlightLength(self):
return self.__l
@property
def Angle(self):
return self.__angle
def calc(self, Pos):
mmperdiv = 2
mmperManipulatorDiv = 0.5
REMPIx = Pos['REMPI']*mmperdiv
Center = Pos['Center ZRM']
Surf = Pos['Surface Y']
REMPIy = (Center - Pos['ZRM'])*2.54
self.__Pos['REMPI'] = (REMPIx, REMPIy)
SurfRef = self.__SurfacePosMeas.Y0
IRRef = self.__SurfacePosMeas.IRPos
SurfPos = (SurfRef - Surf)*mmperManipulatorDiv + IRRef*mmperdiv
self.__Surface = SurfPos
self.__Pos['Surface Beamtool'] = SurfPos
l = sqrt((SurfPos - REMPIx)**2 + REMPIy**2)
angle = degrees(arctan((REMPIy - Pos['ZRM Beam Offset']*2.54)/
(SurfPos - REMPIx)))
self.__REMPIx = REMPIx
self.__REMPIy = REMPIy
return l, angle
def SetRempi(self, horizontal, ZRM):
self.__Pos['REMPI'] = horizontal
self.__Pos['ZRM'] = ZRM
self.__distances = self.calc(self.__Pos)
def visualize(self):
"""
...
"""
fig, ax1, ax2 = self.__plot()
self.savefig = fig.savefig
plt.show(fig)
def __plot(self):
_xlim = (10,-6)
_ylim = (-4,5)
_xticks = range(_xlim[0], _xlim[1], -1)
_yticks = range(_ylim[0], _ylim[1], 1)
fig = plt.figure(figsize=(12,5), dpi=100)
grdspc = gs.GridSpec(1, 2, width_ratios=[2,1])
ax1 = fig.add_subplot(grdspc[0])
ax2 = fig.add_subplot(grdspc[1])
newxax = ax1.twiny()
newyax = ax1.twinx()
ax1.set_title('Beam Position')
ax1.spines['right'].set_visible(False)
ax1.spines['top'].set_visible(False)
ax1.xaxis.set_ticks_position('bottom')
ax1.spines['bottom'].set_position(('data',0))
ax1.yaxis.set_ticks_position('left')
ax1.spines['left'].set_position(('data',0))
ax1.set_xlim(_xlim)
ax1.set_ylim(_ylim)
ax1.xaxis.set_ticks(_xticks)
ax1.xaxis.set_ticklabels([])
ax1.yaxis.set_ticks(_yticks)
ax1.yaxis.set_ticklabels([])
ax2.set_frame_on(False)
for spine in ax2.spines.values():
spine.set_visible(False)
ax2.patch.set_visible(False)
ax2.xaxis.set_ticks([])
ax2.yaxis.set_ticks([])
for ax in [newxax, newyax]:
ax.set_frame_on(True)
ax.spines['right'].set_visible(False)
ax.spines['top'].set_visible(False)
ax.patch.set_visible(False)
newxax.spines['left'].set_visible(False)
newxax.xaxis.set_ticks_position('bottom')
newxax.xaxis.set_label_position('bottom')
newxax.spines['bottom'].set_position(('outward', 10))
newxax.set_xlim(_xlim)
newxax.xaxis.set_ticks(_xticks)
newxax.set_xlabel('Position on Beamtool / div')
newyax.spines['bottom'].set_visible(False)
newyax.yaxis.set_ticks_position('left')
newyax.yaxis.set_label_position('left')
newyax.spines['left'].set_position(('outward', 10))
newyax.set_ylim(_ylim)
newyax.yaxis.set_ticks(_yticks)
newyax.set_ylabel('Position on Beamtool / div')
width = 0.2
height = 2
verts = [
(self.__Surface/2, -height/2), # right bottom
(self.__Surface/2, height/2), # right top
(self.__Surface/2-width, height/2), # left top
(self.__Surface/2-width, -height/2),# left bottom
(0., 0.) #ignored
]
codes = [
Path.MOVETO,
Path.LINETO,
Path.LINETO,
Path.LINETO,
Path.CLOSEPOLY
]
path = Path(verts, codes)
patch = patches.PathPatch(path, facecolor='gold', lw=0)
ax1.add_patch(patch)
ax1.plot(self.__REMPIx/2, self.__REMPIy/2, 'bo', markersize=12)
string = r"""
Positions:
$(x,y)_\mathrm{UV} =\, (%2.2f,\ %2.2f)\ \mathrm{mm}$
$x_\mathrm{S} =\, %2.2f \ \mathrm{mm}$
Angle:
$\theta_\mathrm{f} = \, %2.2f ^\circ$
""" %(self.__REMPIx, self.__REMPIy, self.__Surface, self.__angle)
ax2.annotate(string, xy=(0,0.5), xycoords='axes fraction')
return fig, ax1, ax2
from PyQt4 import Qt
from PyQt4.QtGui import QWidget, QMainWindow, QHBoxLayout, QVBoxLayout
from guiqwt.curve import CurvePlot
from guiqwt.plot import PlotManager
from guiqwt.builder import make
from guiqwt.signals import SIG_RANGE_CHANGED
from guiqwt.shapes import XRangeSelection
from guiqwt.styles import ShapeParam, LineStyleParam
from guiqwt.tools import SelectTool
from numpy import trapz, polyfit, polyval, array, where
from scipy.integrate import quad
class iScopeWidget(QWidget):
"""
Filter testing widget
parent: parent widget (QWidget)
x, y: NumPy arrays
func: function object (the signal filter to be tested)
"""
def __init__(self, parent, x, y):
QWidget.__init__(self, parent)
self.setMinimumSize(320, 200)
self.x = x
self.y = y
#---guiqwt related attributes:
self.plot = None
self.curve_item = None
#---
def setup_widget(self):
#---Create the plot widget:
x = self.x
y = self.y
self.plot = CurvePlot(self)
self.curve_item = make.curve([], [], color='b')
self.plot.add_item(self.curve_item)
self.plot.set_antialiasing(True)
width = x[-1] - x[0]
self.intrange = make.range(x[0]+0.4*width, x[-1]-0.4*width)
self.plot.add_item(self.intrange)
self.lbgrange = make.range(x[0]+0.3*width, x[-1]-0.65*width)
self.plot.add_item(self.lbgrange)
self.lbgrange.pen = Qt.QPen(Qt.QColor('blue'))
self.lbgrange.brush = Qt.QBrush(Qt.QColor(0,0,120,100))
self.rbgrange = make.range(x[0]+0.7*width, x[-1]-0.1*width)
self.rbgrange.pen = Qt.QPen(Qt.QColor('blue'))
self.rbgrange.brush = Qt.QBrush(Qt.QColor(0,0,120,100))
self.label1 = make.label(r"", "TR", (0, 0), "TR")
self.plot.add_item(self.rbgrange)
self.bg_item = make.curve([], [], color='r')
self.plot.add_item(self.bg_item)
self.fit_bg()
self.plot.add_item(self.label1)
self.connect(self.plot, SIG_RANGE_CHANGED, self.fit_bg)
#---
vlayout = QVBoxLayout()
vlayout.addWidget(self.plot)
self.setLayout(vlayout)
self.update_curve()
def fit_bg(self):
degree = 3
table = array([self.x, self.y])
low, high = self.lbgrange.get_range()
idxlower = set(where(table[0]<=high)[0])
idxhigher = set(where(table[0]>=low)[0])
idx1 = list(idxhigher.intersection(idxlower))
low, high = self.rbgrange.get_range()
idxlower = set(where(table[0]<=high)[0])
idxhigher = set(where(table[0]>=low)[0])
idx2 = list(idxhigher.intersection(idxlower))
idx = idx1 + idx2
x, y = table[:, idx]
self.coeff = polyfit(x, y, degree)
left, right = self.intrange.get_range()
#bg = abs(quad(lambda x: polyval(self.coeff, x), left, right)[0])
idxlower = set(where(table[0]<=right)[0])
idxhigher = set(where(table[0]>=left)[0])
idx = list(idxhigher.intersection(idxlower))
x, y = table[:, idx]
self.int = abs(trapz(y-polyval(self.coeff, x), x=x))
self.update_label()
self.update_curve()
def update_label(self):
self.label1.set_text(u"""trapz(red) - int(blue) = %e""" % self.int)
def update_curve(self):
#---Update curve
self.curve_item.set_data(self.x, self.y)
self.plot.replot()
y = polyval(self.coeff, self.x)
self.bg_item.set_data(self.x, y)
class iScope(QMainWindow):
def __init__(self):
QMainWindow.__init__(self)
self.setWindowTitle("iScope (TM)")
hlayout = QHBoxLayout()
central_widget = QWidget(self)
central_widget.setLayout(hlayout)
self.setCentralWidget(central_widget)
#---guiqwt plot manager
self.manager = PlotManager(self)
#---
def add_plot(self, x, y):
widget = iScopeWidget(self, x, y)
widget.setup_widget()
self.centralWidget().layout().addWidget(widget)
#---Register plot to manager
self.manager.add_plot(widget.plot)
#---
def setup_window(self):
#---Add toolbar and register manager tools
toolbar = self.addToolBar("tools")
self.manager.add_toolbar(toolbar, id(toolbar))
self.manager.register_standard_tools()
self.manager.tools[0].activate()
from PyQt4.QtGui import QApplication
from numpy import loadtxt
from helper import construct_filename
def IntegrateScopeTrace(fileprefix, filenumbers):
intensities = []
for dat in [loadtxt(filename, unpack=True) for filename in
construct_filename(fileprefix, filenumbers)]:
x, y = dat
app = QApplication.instance()
if not app:
app = QApplication([])
win = iScope()
win.add_plot(x*1e6, y)
#---Setup window
win.setup_window()
win.resize(800,600)
#---
win.show()
try:
app.exec_()
intensities.append(win.centralWidget().layout().itemAt(0).widget().int)
except:
pass
print 'Number of elements: %d' % len(intensities)
print intensities
# TESTCODE
if __name__ == '__main__':
from tof_analysis import SurfacePosMeas
angles = linspace(-45, 45, 17)
signal = -cos(radians(angles+8))**12
print signal
pos = arange(1,9.5,0.5)
surfpos = arange(30,33,0.2)
power = [0.3, 0.3, 0.285, 0.275, 0.255, 0.24, 0.23, 0.2, .179, .155,
.129, .107, .082, .066, .047]
SPM1 = SurfacePosMeas(surfpos, power, IRPos=7)
Setups = [REMPISetup(SPM1, {'REMPI': 0, 'Center ZRM': 5.1, 'ZRM': zrm,
'Surface Y': 35}) for zrm in pos]
AngDistr = AngularDistribution(Setups, signal)