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Commit 7196bc17 authored by Daniel Toyra's avatar Daniel Toyra
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Updated and commented methods in pykat.optics.maps, mainly surfacemap.remove_curvature().

parent 98f37ee8
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pykat/optics/maps.py
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......@@ -328,7 +328,7 @@ class surfacemap(object):
ymax = len(self.y)-1
ylim = [self.y.min()*100, self.y.max()*100]
# ALSO (SEE LONG TEXT BELOW) ADDED BY DT TO FIX LIMITS
# ALSO ADDED (SEE LONG TEXT BELOW) BY DT TO FIX LIMITS
# ------------------------------------------------------
xlim,ylim = ylim,xlim
# ------------------------------------------------------
......@@ -381,54 +381,116 @@ class surfacemap(object):
def remove_curvature(self, Rc0, w=0, display='off'):
# Removes curvature from mirror map by fitting a sphere to
# mirror surface. Based on the file
# 'FT_remove_curvature_from_mirror_map.m'.
# Rc0 - Initial guess of the radius of curvature
# w - Beam radius on mirror [m], used for weighting. w=0
# switches off weighting.
# display - Display mode of the fitting routine. Can be 'off',
# 'iter', 'notify', or 'final'.
# z-value at centre of the mirror.
zOffset = self.data[round(self.center[1]), round(self.center[0])]
def remove_curvature(self, Rc0, w=None, zOffset=None, isCenter=[False,False],
display='off'):
'''
Removes curvature from mirror map by fitting a sphere to
mirror surface. Based on the file 'FT_remove_curvature_from_mirror_map.m'.
Rc0 - Initial guess of the radius of curvature [m]
w - Beam radius on mirror [m], used for weighting.
zOffset - Initial guess of the z-offset [surfacemap.scaling]. Generally not needed.
isCenter - 2D-list with booleans. isCenter[0] Determines if the center of the
sphere is fitted (True) or not (False, recommended). If the center is
fitted, then isCenter[1] determines if the weights are centered around
the fitted center (True) or centered around the center of the data-grid
(False, highly recommended).
display - Display mode of the fitting routine. Can be 'off',
'iter', 'notify', or 'final'.
'''
# z-value at centre of the data-grid. Serves as initial guess for deviation
# from z=0, if no other first guess is given.
if zOffset is None:
zOffset = self.data[round(self.center[1]), round(self.center[0])]
# If fitting center of the sphere, four variables are fitted. Initial guess
# of deviation from notNan-data-grid-center: (x0,y0) = (0,0).
if isCenter[0]:
params = [Rc0, zOffset, 0.0, 0.0]
# Otherwise two.
else:
params = [Rc0, zOffset]
# Grid with X,Y and r2 = (X^2+Y^2) values. X and Y crosses zero in the center
# of the xy-plane.
X,Y,r2 = self.createGrid()
# Cost-function to minimize.
def costFunc(params):
n = len(params)
if n==2:
# If the center of the mirror is fitted, four variables are fitted.
if isCenter[0]:
Rc = params[0]
zOffset = params[1]
x0 = 0
y0 = 0
x0 = params[2]
y0 = params[3]
# Otherwise 2 variables.
else:
Rc = params[0]
zOffset = params[1]
x0 = params[2]
y0 = params[3]
x0 = 0
y0 = 0
Z = self.createSphere(Rc,X,Y,zOffset,x0,y0)
if w==0:
if w is None:
# Mean squared difference between map and the created sphere.
res = math.sqrt( ((self.data[self.notNan] -
Z[self.notNan])**2).sum() )/self.notNan.sum()
else:
weight = 2/(math.pi*w**2)*np.exp(-2*r2/w**2)
if isCenter[0] and isCenter[1]:
# Weights centered around fitting spehere center. May give weird
# results if the mirror deviates much from a sphere.
weight = (2/(math.pi*w**2))*np.exp(-2*( (X-x0)**2 + (Y-y0)**2 )/w**2)
else:
# Weights centered around the center of the mirror xy-plane.
weight = (2/(math.pi*w**2))*np.exp(-2*r2/w**2)
# Weighted mean squared difference between map and the created sphere.
res = math.sqrt( (weight[self.notNan]*((self.data[self.notNan] -
Z[self.notNan])**2)).sum() )/self.notNan.sum()
print(Rc,zOffset,res)
Z[self.notNan])**2)).sum() )/weight[self.notNan].sum()
return res
params = [Rc0,zOffset]
# Using the simplex Nelder-Mead method. This is the same or very
# similar to the method used in 'FT_remove_curvature_from_mirror_map.m',
# but there are probably better methods to use.
out = minimize(costFunc, params, method='Nelder-Mead',tol=1.0e-6)
Rc = out['x'][0]
zOffset = out['x'][1]
Z = self.createSphere(Rc,X,Y,zOffset)
self.data[self.notNan] = self.data[self.notNan]-Z[self.notNan]
return self.data, self.Rc, self.zOffset
# Assigning values to the instance variables
self.Rc = out['x'][0]
self.zOffset = out['x'][1]
# If center was fitted, assign new values to instance variable center, and
# subtract the fitted sphere from the mirror map.
if isCenter[0]:
x0 = out['x'][2]
y0 = out['x'][3]
# Converts the deviation into a new absolut center in data points.
self.center = (self.center[0] + x0/self.step_size[0],
self.center[1] + y0/self.step_size[1])
# Creating fitted sphere
Z = self.createSphere(self.Rc, X, Y, self.zOffset, x0, y0)
# Subtracting sphere from map
self.data[self.notNan] = self.data[self.notNan]-Z[self.notNan]
return self.Rc, self.zOffset, x0, y0
# Subtracting fitted sphere from mirror map.
else:
# Creating fitted sphere
Z = self.createSphere(self.Rc,X,Y,self.zOffset)
# Subtracting sphere from map
self.data[self.notNan] = self.data[self.notNan]-Z[self.notNan]
return self.Rc, self.zOffset
def createSphere(self,Rc,X,Y,zOffset=0,x0=0,y0=0,xTilt=0,yTilt=0,isPlot=False):
# Creating spherical surface. Based on 'FT_create_sphere_for_map.m'
'''
Creating spherical surface. Based on 'FT_create_sphere_for_map.m'
Rc - Radius of curvature, and center of sphere on z-axis in case zOffset=0 [m].
X, Y - Matrices of x,y-values generated by 'X,Y = numpy.meshgrid(xVec,yVec)'.
Preferrably created by method 'surfacemap.createGrid()' [m].
zOffset - Surface center offset from 0. Positive value gives the surface center
positive z-coordinate. [self.scaling]
x0,y0 - The center of the sphere in the xy-plane.
x/yTilt - Tilt of x/y-axis [rad].
isPlot - Plot or not [boolean]. Not recommended when used within optimization
algorithm.
'''
# Adjusting for tilts and offset
Z = zOffset + (X*np.tan(xTilt) + Y*np.tan(yTilt))/self.scaling
......@@ -442,15 +504,22 @@ class surfacemap(object):
axes = pylab.pcolormesh(X, Y, Z) #, vmin=zmin, vmax=zmax)
cbar = fig.colorbar(axes)
cbar.set_clim(Z.min(), Z.max())
pylab.title('Z_min = ' + str(Z.min()) + ' Z_max = ' + str(Z.max()))
pylab.title('Z_min = ' + str(Z.min()) + ' Z_max = ' + str(Z.max()))
pylab.show()
return Z
def createGrid(self):
# Creating grid for the map. Based on 'FT_create_grid_for_map.m'
# and 'FT_init_grid.m'.
# ----------------------------------------------------------------
'''
Creating grid for fitting spherical surface to the map. Based on
'FT_create_grid_for_map.m' and 'FT_init_grid.m'. (x,y) = (0,0) is
placed at the centre of the mirror surface defined by the instance
variable surfacemap.center.
Returns X,Y,r2
, where X,Y = numpy.meshgrid(x,y), and r2 = X^2 + Y^2.
'''
yPoints, xPoints = self.data.shape
# Difference between the data point centre, and the centre of
# the mirror surface.
......@@ -461,22 +530,18 @@ class surfacemap(object):
x = np.array([n for n in range(xPoints)])
y = np.array([n for n in range(yPoints)])
# Shouldn't the real physical size be (points-1)*step_size?
# Physical size. Shouldn't this be (points-1)*step_size?
xSize = xPoints*self.step_size[0]
ySize = yPoints*self.step_size[1]
# ...corrected here by subracting one step. Isn't this unnecessary
# complicated btw?
xAxis = x*self.step_size[0] + xOffset - (xSize-self.step_size[0])/2
yAxis = y*self.step_size[1] + yOffset - (ySize-self.step_size[1])/2
#print(xAxis[round(self.center[0])-1:round(self.center[0])+2])
#print(yAxis[round(self.center[1])-1:round(self.center[1])+2])
X,Y = np.meshgrid(xAxis,yAxis)
r = np.sqrt(X**2 + Y**2)
r2 = X**2 + Y**2
phi = np.arctan2(Y,X)
print(X.min(),X.max(),Y.min(),Y.max())
# r = np.sqrt(X**2 + Y**2)
# phi = np.arctan2(Y,X)
return X,Y,r2
# ----------------------------------------------------------------
......@@ -819,13 +884,20 @@ class zernikemap(surfacemap):
self.data = data
# Reads surface map files and return surfacemap-object.
# supported mapFormat: 'finesse', 'ligo', 'zygo'.
# All ascii formats.
def read_map(filename, mapFormat='finesse'):
# Function turning input x into float.
g = lambda x: float(x)
def read_map(filename, mapFormat='finesse', scaling=1.0e-9):
'''
Reads surface map files and return a surfacemap-object xy-centered at the
center of the mirror surface.
filename - name of surface map file.
mapFormat - 'finesse', 'ligo', 'zygo'. Currently only for ascii formats.
scaling - scaling of surface height of the mirror map [m].
'''
# Function converting string number into float.
g = lambda x: float(x)
# Reads finesse mirror maps.
if mapFormat == 'finesse':
with open(filename, 'r') as f:
......@@ -838,13 +910,11 @@ def read_map(filename, mapFormat='finesse'):
step = tuple(map(g, f.readline().split(':')[1].strip().split()))
scaling = float(f.readline().split(':')[1].strip())
data = np.loadtxt(filename, dtype=np.float64,ndmin=2,comments='%')
# Converts raw zygo and ligo mirror maps to the finesse
# format. Based on translation of the matlab scripts
# 'FT_read_zygo_map.m' and 'FT_read_ligo_map.m'
# format. Based on the matlab scripts 'FT_read_zygo_map.m' and
# 'FT_read_ligo_map.m'.
elif mapFormat == 'ligo' or mapFormat == 'zygo':
if mapFormat == 'ligo':
isLigo = True
......@@ -861,7 +931,8 @@ def read_map(filename, mapFormat='finesse'):
else:
isAscii = False
# Unknowns (why are these values hard coded here?)
# Unknowns (why are these values hard coded here?) Moving
# scaling to input. Fix the others later too.
# ------------------------------------------------------
# Standard maps have type 'phase' (they store surface
# heights)
......@@ -870,7 +941,7 @@ def read_map(filename, mapFormat='finesse'):
# affected
field = 0
# Measurements in nanometers
scaling = 1.0e-9
# scaling = 1.0e-9
# ------------------------------------------------------
# Reading header of LIGO-map (Zygo file? Says Zygo in
......@@ -890,7 +961,7 @@ def read_map(filename, mapFormat='finesse'):
iRows = float(line.split()[3])
line = f.readline().split()
# Unknown
# Unknown usage.
# ----------------------------------------------
if isLigo:
y0 = float(line[0])
......
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