ax = fig1.add_subplot(111, projection='3d')
ax.scatter(x, y, z, zdir='z', c= 'red')
#detector size in pixels
detX = 500.
detY = 500.
#in meters
waveLength = 0.7293*(10**(-10)) # wavelength of x-ray beam
detDist = 0.002 # detector distance
pixSz = 0.0003 # pixel size
atmFactor = 1 # atomic form factor
atmDist = 2.*10**-10
# number of unit cells per side on a block, user defined
cell_per_side_x = 2
cell_per_side_y = 2
cell_per_side_z = 2
#particle = createParticle(cell_per_side_x, cell_per_side_y, cell_per_side_z)
#diffract = calculateReciprocal(particle)
plots_q = find_q_plots(detX, detY, pixSz, detDist, waveLength)
plot_q_plots(plots_q[0], plots_q[1], plots_q[2])
#plot2D(diffract, detDist)
#plot3D(diffract)
plt.show()
xyzA[:,:3] = xyz_rot
np.savetxt( 'cor_file_rot.coor', xyzA )
numRotations = 2
intensities = []
for rotation in xrange(numRotations):
#xyzA[:,:3] = rotateRand(xyzA[:,:3])
rotateRand()
detX = 515
detY = 515
waveLength = 0.7293 # wavelength of x-ray beam angstroms
detDist = 0.02 # detector distance meters
pixSz = 0.0003 # pixel size meters
qx,qy,qz, q = find_q_plots(detX, detY, pixSz, detDist, waveLength)
x,y,z, id = np.loadtxt(r'cor_file_rot.coor', unpack = True)
factors = findAtmFact(pixSz, detDist, waveLength, detX, detY, id)
atomTypes, atmFactors = factors[1], factors[0]
I = np.zeros([detY, detX], dtype = np.complex128)
for i in xrange(detX):
for j in xrange(detY):
for k in xrange(x.shape[0]):
typeIndex = atomTypes.index( id[k] )
atmFactor = find_nearest(atmFactors[:,typeIndex],q[j,i] )
I[j,i] += atmFactor*cmath.exp(complex(0,-1)*(qx[j,i]*x[k]+qy[j,i]*y[k]+qz[j,i]*z[k]))
I[j,i] = np.abs(I[j,i])**2
I = np.real(I)
