def __init__(self, axis=None, angle=None, R=None):
if isinstance(R, dnp.ndarray):
if R.shape != (3, 3):
raise Exception('R must be a 3 by 3 matrix')
self.R = R
angle = dnp.arccos(0.5*(sum(dnp.diag(R))-1))
self.angle = float(dnp.rad2deg(angle))
x = (R[2][1]-R[1][2])/(2*dnp.sin(angle))
y = (R[0][2]-R[2][0])/(2*dnp.sin(angle))
z = (R[1][0]-R[0][1])/(2*dnp.sin(angle))
axis = Vector(x,y,z)
axis = axis.unit()
self.axis = axis
return
if isinstance(angle, dnp.ndarray):
angle = angle[0]
elif isinstance(angle, int):
angle = float(angle)
if not isinstance(angle, float):
raise Exception('angle must be a float not {}'.format(type(angle)))
axis = axis.unit()
self.axis = axis
self.angle = angle
angle = float(dnp.radians(angle))
M = dnp.array([[0.0, -axis.z, axis.y],
[axis.z, 0.0, -axis.x],
[-axis.y, axis.x, 0.0]])
N = axis.tensor_product(axis)
I = dnp.identity(3)
self.R = I*dnp.cos(angle) + M*dnp.sin(angle) + (1-dnp.cos(angle))*N
angle = 56
def dofourier(xarray, yarray, printres=False):
nvals = len(yarray)
avht = yarray.mean()
angles = dnp.linspace(0, 2 * dnp.pi, len(yarray))
# print angles
ycarray = yarray - avht
cosines = dnp.cos(angles)
sines = dnp.sin(angles)
cosint = cosines * ycarray
sinint = sines * ycarray
if printres:
print "Yarray:", yarray
print "Ycarray:", ycarray
print "Sinint:", sinint
print "Cosint:", cosint
cosum = cosint[:-1].sum()
sinsum = sinint[:-1].sum()
cosfactor = cosum / float(nvals - 1)
sinfactor = sinsum / float(nvals - 1)
if printres:
print "sinfactor, cosfactor: %.4f %.4f" % (sinfactor, cosfactor)
ratio = sinfactor / cosfactor
delta = math.atan(ratio)
deltadeg = math.degrees(delta)
if printres:
print "Delta degrees %06.4f" % deltadeg
halfmag = math.sqrt(sinfactor ** 2 + cosfactor ** 2)
mag = 2.0 * halfmag
if printres:
print "Magnitude: %06.4f" % mag
print "vertical centre %7.4f" % avht
calcresult = avht + mag * dnp.cos(angles - delta)
if printres:
print "Calcresult:", calcresult
for idx in range(0, len(yarray)):
print yarray[idx], calcresult[idx]
return (avht, mag, delta, calcresult)
def dofourier(xarray,yarray,printres=False):
nvals=len(yarray)
avht=yarray.mean()
angles=dnp.linspace(0,2*dnp.pi,len(yarray))
#print angles
ycarray=yarray-avht
cosines=dnp.cos(angles)
sines=dnp.sin(angles)
cosint=cosines*ycarray
sinint=sines*ycarray
if printres:
print "Yarray:",yarray
print "Ycarray:",ycarray
print "Sinint:",sinint
print "Cosint:",cosint
cosum=cosint[:-1].sum()
sinsum=sinint[:-1].sum()
cosfactor=cosum/float(nvals-1)
sinfactor=sinsum/float(nvals-1)
if printres:
print "sinfactor, cosfactor: %.4f %.4f"%(sinfactor,cosfactor)
ratio=sinfactor/cosfactor
delta=math.atan(ratio)
deltadeg=math.degrees(delta)
if printres:
print"Delta degrees %06.4f"%deltadeg
halfmag=math.sqrt(sinfactor**2+cosfactor**2)
mag=2.0*halfmag
if printres:
print"Magnitude: %06.4f"%mag
print "vertical centre %7.4f"%avht
calcresult=avht+mag*dnp.cos(angles-delta)
if printres:
print"Calcresult:",calcresult
for idx in range(0,len(yarray)):
print yarray[idx],calcresult[idx]
return(avht,mag,delta,calcresult)
def readTestInputs(
filename="height.txt",
idealname="ideal.txt",
visit_directory="/dls/i12/data/2014/cm4963-2",
input_directory="tmp",
printres=False,
):
infilename = "%s/%s/%s" % (visit_directory, input_directory, filename)
idealfilename = "%s/%s/%s" % (visit_directory, input_directory, idealname)
inlist = []
ideallist = []
try:
infile = open(infilename, "r")
except:
print ("File %s not opened properly" % infilename)
return None
n = 0
for line in infile:
if printres:
print n, line
n = n + 1
inlist.append(float(line))
infile.close()
try:
infile = open(idealfilename, "r")
except:
print ("File %s not opened properly" % idealfilename)
return None
for line in infile:
if printres:
print n, line
n = n + 1
ideallist.append(float(line))
infile.close()
if printres:
print inlist
print ideallist
inarray = dnp.array(inlist)
idealarray = dnp.array(ideallist)
print len(inarray)
angarray = dnp.linspace(0, dnp.pi * 2.0, len(inarray), True)
horizarray = 2500.0 * dnp.cos(angarray)
ofile = open("%s/%s/testpoints.txt" % (visit_directory, input_directory), "w")
ofile.write("angle,X,idealY,noisyY\n")
for i in range(0, len(angarray)):
ofile.write("%g,%g,%g,%g\n" % (angarray[i], horizarray[i], idealarray[i], inarray[i]))
ofile.close()
return (horizarray, inarray, idealarray)
def readTestInputs(filename='height.txt',idealname='ideal.txt',visit_directory='/dls/i12/data/2014/cm4963-2',input_directory='tmp',printres=False):
infilename="%s/%s/%s"%(visit_directory,input_directory,filename)
idealfilename="%s/%s/%s"%(visit_directory,input_directory,idealname)
inlist=[]
ideallist=[]
try:
infile=open(infilename,'r')
except:
print("File %s not opened properly"%infilename)
return(None)
n=0
for line in infile:
if printres:
print n,line
n=n+1
inlist.append(float(line))
infile.close()
try:
infile=open(idealfilename,'r')
except:
print("File %s not opened properly"%idealfilename)
return(None)
for line in infile:
if printres:
print n,line
n=n+1
ideallist.append(float(line))
infile.close()
if printres:
print inlist
print ideallist
inarray=dnp.array(inlist)
idealarray=dnp.array(ideallist)
print len(inarray)
angarray=((dnp.linspace(0,dnp.pi*2.0,len(inarray),True)))
horizarray=2500.0*dnp.cos(angarray)
ofile=open("%s/%s/testpoints.txt"%(visit_directory,input_directory),'w')
ofile.write("angle,X,idealY,noisyY\n")
for i in range(0,len(angarray)):
ofile.write("%g,%g,%g,%g\n"%(angarray[i],horizarray[i],idealarray[i],inarray[i]))
ofile.close()
return(horizarray,inarray,idealarray)
def python_cos(ds):
'''Performs a cos() on ds input'''
return dnp.cos(ds)
def project(self, energy, UB, pixels, gamma, delta, omega, alpha, nu):
# put the detector at the right position
dx, dy, dz = pixels
# convert angles to radians
gamma, delta, alpha, omega, nu = numpy.radians(
(gamma, delta, alpha, omega, nu))
RGam = numpy.matrix([[1, 0, 0], [0, cos(gamma), -sin(gamma)],
[0, sin(gamma), cos(gamma)]])
RDel = (numpy.matrix([[cos(delta), -sin(delta), 0],
[sin(delta), cos(delta), 0], [0, 0, 1]])).getI()
RNu = numpy.matrix([[cos(nu), 0, sin(nu)], [0, 1, 0],
[-sin(nu), 0, cos(nu)]])
# calculate Cartesian coordinates for each pixel using clever matrix stuff
M = numpy.mat(
numpy.concatenate(
(dx.flatten(0), dy.flatten(0),
dz.flatten(0))).reshape(3, dx.shape[0] * dx.shape[1]))
XYZp = RGam * RDel * RNu * M
xp = dnp.array(XYZp[0]).reshape(dx.shape)
yp = dnp.array(XYZp[1]).reshape(dy.shape)
zp = dnp.array(XYZp[2]).reshape(dz.shape)
# don't bother with the part about slits...
# Calculate effective gamma and delta for each pixel
d_ds = dnp.sqrt(xp**2 + yp**2 + zp**2)
Gam = dnp.arctan2(zp, yp)
Del = -1 * dnp.arcsin(-xp / d_ds)
# wavenumber
k = 2 * math.pi / 12.398 * energy
# Define the needed matrices. The notation follows the article by Bunk &
# Nielsen. J.Appl.Cryst. (2004) 37, 216-222.
M1 = k * numpy.matrix(
cos(omega) * sin(Del) - sin(omega) *
(cos(alpha) *
(cos(Gam) * cos(Del) - 1) + sin(alpha) * sin(Gam) * cos(Del)))
M2 = k * numpy.matrix(
sin(omega) * sin(Del) + cos(omega) *
(cos(alpha) *
(cos(Gam) * cos(Del) - 1) + sin(alpha) * sin(Gam) * cos(Del)))
M3 = k * numpy.matrix(-sin(alpha) * (cos(Gam) * cos(Del) - 1) +
cos(alpha) * sin(Gam) * cos(Del))
# invert UB matrix
UBi = numpy.matrix(UB).getI()
# calculate HKL
H = UBi[0, 0] * M1 + UBi[0, 1] * M2 + UBi[0, 2] * M3
K = UBi[1, 0] * M1 + UBi[1, 1] * M2 + UBi[1, 2] * M3
L = UBi[2, 0] * M1 + UBi[2, 1] * M2 + UBi[2, 2] * M3
return (H, K, L)
def python_cos(ds):
'''Performs a cos() on ds input'''
return dnp.cos(ds)
def project(self, energy, UB, pixels, gamma, delta, omega, alpha, nu):
# put the detector at the right position
dx,dy,dz = pixels
# convert angles to radians
gamma, delta, alpha, omega, nu = numpy.radians((gamma, delta, alpha, omega, nu))
RGam = numpy.matrix([[1,0,0],[0,cos(gamma),-sin(gamma)],[0,sin(gamma),cos(gamma)]])
RDel = (numpy.matrix([[cos(delta),-sin(delta),0],[sin(delta),cos(delta),0],[0,0,1]])).getI()
RNu = numpy.matrix([[cos(nu),0,sin(nu)],[0,1,0],[-sin(nu),0,cos(nu)]])
# calculate Cartesian coordinates for each pixel using clever matrix stuff
M = numpy.mat(numpy.concatenate((dx.flatten(0), dy.flatten(0), dz.flatten(0))).reshape(3,dx.shape[0]*dx.shape[1]))
XYZp = RGam * RDel * RNu * M
xp = dnp.array(XYZp[0]).reshape(dx.shape)
yp = dnp.array(XYZp[1]).reshape(dy.shape)
zp = dnp.array(XYZp[2]).reshape(dz.shape)
# don't bother with the part about slits...
# Calculate effective gamma and delta for each pixel
d_ds = dnp.sqrt(xp**2 + yp**2 + zp**2)
Gam = dnp.arctan2(zp, yp)
Del = -1 * dnp.arcsin(-xp/d_ds)
# wavenumber
k = 2 * math.pi / 12.398 * energy
# Define the needed matrices. The notation follows the article by Bunk &
# Nielsen. J.Appl.Cryst. (2004) 37, 216-222.
M1 = k * numpy.matrix(cos(omega) * sin(Del) - sin(omega) * (cos(alpha) * (cos(Gam) * cos(Del)-1) + sin(alpha) * sin(Gam) * cos(Del)))
M2 = k * numpy.matrix(sin(omega) * sin(Del) + cos(omega) * (cos(alpha) * (cos(Gam) * cos(Del)-1) + sin(alpha) * sin(Gam) * cos(Del)))
M3 = k * numpy.matrix(-sin(alpha) * (cos(Gam) * cos(Del)-1) + cos(alpha) * sin(Gam) * cos(Del))
# invert UB matrix
UBi = numpy.matrix(UB).getI()
# calculate HKL
H = UBi[0,0]*M1 + UBi[0,1]*M2 + UBi[0,2]*M3
K = UBi[1,0]*M1 + UBi[1,1]*M2 + UBi[1,2]*M3
L = UBi[2,0]*M1 + UBi[2,1]*M2 + UBi[2,2]*M3
return (H, K, L)