def sseed_2(input_file,
output_files,
E_ev,
chicane,
run_dir,
delay=0.0,
debug=True,
output_file=None,
xt_couple=False,
filterfilename='',
method='hxr_wake_calc',
paral=False):
h = 4.135667516e-15
c = 299792458.0
g = readGenesisOutput(input_file, readall=0)
print 'read sliced field ', g('ncar'), g.nSlices
ncar = int(g('ncar'))
dgrid = float(g('dgrid'))
xlamds = float(g('xlamds'))
#nslice = len(g.spec)
nslice = int(g.nSlices)
print 'nslice = ', nslice
zsep = float(g('zsep'))
print zsep
k0 = 2 * np.pi / xlamds
ds = zsep * xlamds #interval ds
srange = nslice * zsep * xlamds #range in s
dkold = 2 * np.pi / srange
krange = dkold * nslice
#idx_max = np.argmax(g.I)
#s_imax = -srange/2.0 + idx_max*ds
#SHF = np.int((delay-s_imax)/ds)
SHF = int(delay) #np.int(delay/ds) #or divided ds
#print 'imax = ', idx_imax
#print 'delay = ', delay
#print 'delay-s_imax', delay-s_imax
#print 'SHF*ds', SHF*ds
#SHF = np.int((-0.5e-5+s_imax)/ds)
####SHF = np.int((delay)/ds)
#print np.int((delay+s_imax)/ds)*ds
#print 'due=', SHF*ds
#exit()
#g.idx_max = idx_max
#print 'ss idx_max:', g.idx_max
if method == 'hxr_wake_calc':
r = Ray()
r.lamb = 2 * pi * hbar * c / E_ev
print 'wavelength', r.lamb, '(', E_ev, 'eV), filetring...'
ref_idx = chicane.cryst.ref_idx
filt = get_crystal_filter(chicane.cryst, r, nk=1000, ref_idx=ref_idx)
chicane.cryst.filter = filt
klpos, krpos, cwidth = FWHM(filt.k, 1.0 - np.abs(filt.tr))
cmid_idx = int((krpos - klpos) / 2.0)
cmid = filt.k[cmid_idx]
H, d, phi = find_bragg(lambd=r.lamb,
lattice=chicane.cryst.lattice,
ord_max=15)
dhkl = d[ref_idx]
thetaB = phi[ref_idx] * np.pi / 180.0
dk = cwidth / 6.0 #The filter transmissivity defines this quantity by taking 5 points on the bottom of T; if not good separation, must tune!!!
dr = ncar / (
dgrid * np.tan(thetaB)
) #dr prepares for inclusion of the spatiotemporal coupling; it is transverse pix size/cot(thetaB)
#dr=1.0
print '#################'
print 'dgrid = ', dgrid
print 'ncar = ', ncar
print 'dr = ', dr
print 'thetaB = ', thetaB
print 'ds = ', ds
print 'SHF = ', SHF
print '#################'
mult = np.int(dkold / dk)
if int(mult / 2) - mult / 2 == 0: mult = mult - 1
if mult == 0: mult = 1
print 'MULT = ', mult
dk = dkold / mult #Important! Otherwise the np.int in the line changes the k scale substantially
phases = unfold_angles(np.angle(np.conj(filt.tr)))
f1 = open(output_files[1], 'w')
f2 = open(output_files[2], 'w')
for i in range(len(filt.k)):
f1.write('%s ' % (filt.k[i]) + '%s' % np.abs(filt.tr[i]) + '\n')
f2.write('%s ' % (filt.k[i]) + '%s' % phases[i] + '\n')
f1.close()
f2.close()
if method == 'sxr_filter_read':
# f = open(filterfilename, 'r')
#[abs, dlpl]
# import numpy as np
# from math import pi
# E_ev=1000.
#icf_path='d:\Work\!PROJECTS\ocelot_test\ICF_1000.ascii'
f = open(filterfilename, 'r')
data = np.genfromtxt(f, delimiter=',')
#delete(data,0,0) # Erases the first row (i.e. the header)
#plot(data[:,0],data[:,1],'o')
f.close()
dlpl = np.flipud(data[:, 0])
Tmod = np.flipud(data[:, 1])
Tpha = np.zeros(len(data[:, 0]))
lambda_0 = 1239.8 / E_ev * 1e-9
k = 2 * pi / (lambda_0 + lambda_0 * dlpl)
dk_f = k[0] - k[1]
k = np.concatenate(([k[0] + dk_f], k, [k[-1] - dk_f]))
Tmod = np.concatenate(([0], Tmod, [0]))
Tpha = np.concatenate(([0], Tpha, [0]))
# Tmod=np.insert(Tmod,slice(0),0)
# Tmod=np.insert(Tmod,slice(-1),0)
# Tpha=np.insert(Tmod,slice(0),0)
# Tpha=np.insert(Tmod,slice(-1),0)
# Tmod=np.insert(Tmod,slice(0,-1),[0,0])
# Tpha=np.insert(Tpha,slice(0,-1),[0,0])#padding with zeros on edges, so that interpolation was done with zeros as well
print np.column_stack((k, Tmod))
#f = open(res_dir+'s2.Tmod.dat', 'w')
# writepath_Tmod='d:\Work\!PROJECTS\ocelot_test\s2.Tmod.dat'
# writepath_Tpha='d:\Work\!PROJECTS\ocelot_test\s2.Tpha.dat'
np.savetxt(output_files[1], np.column_stack((k, Tmod)))
np.savetxt(output_files[2], np.column_stack((k, Tpha)))
klpos, krpos, cwidth = FWHM(k, Tmod)
cwidth = abs(cwidth)
print 'CWIDTH=', cwidth
dk = cwidth / 10.0
mult = np.int(dkold / dk)
#if int(mult/2) - mult/2 ==0: mult = mult-1 %probably it needs to be even
print 'MULT = ', mult
dk = dkold / mult #Important! Otherwise the np.int in the line changes the k scale substantially
# bring to common format !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
dr = 0
# phases = unfold_angles(np.angle(np.conj(filt.tr)))
if paral == True:
ARGS = ''.join([
input_file + '.dfl' + ' ', output_files[0] + ' ',
output_files[1] + ' ', output_files[2] + ' ',
output_files[3] + ' ', output_files[4] + ' ',
output_files[5] + ' ', output_files[6] + ' ',
output_files[7] + ' ', output_files[8] + ' ',
str(xlamds) + ' ',
str(ncar) + ' ',
str(mult) + ' ',
str(ds) + ' ',
str(dk) + ' ',
str(SHF) + ' ',
str(nslice) + ' ',
str(dr)
])
runpar = '`which mpirun` -x PATH -x MPI_PYTHON_SITEARCH -x PYTHONPATH'
prog = ' ' + 'python /data/netapp/xfel/gianluca/products/ocelot/utils/seed.py ' + ARGS + ''
#prog = ' '+'python /data/netapp/xfel/svitozar/CODE/ocelot/utils/seed.py '+ARGS+''
#print 'NEWARGS'
#print ARGS
#exit()
cmd = runpar + prog
os.system(cmd)
if paral == False:
import seed0 as sd
sd.filterfield(
input_file + '.dfl',
output_files[0],
output_files[1],
output_files[2],
output_files[3],
output_files[4],
output_files[5],
output_files[6],
output_files[7],
output_files[8],
#output_files[9],
#output_files[10],
#output_files[11],
#output_files[12],
#output_files[13],
#output_files[14],
#output_files[15],
#output_files[16],
xlamds,
ncar,
mult,
ds,
dk,
SHF,
nslice,
dr)
print 'reading filtered file (hxrss_common, lile 728) ', output_files[5]
ssc, Pout = readres(output_files[5])
lsc, Sout = readres(output_files[7])
return ssc, Pout, lsc, Sout
#geo = Geometry([m2])
return geo
geo = init_geometry()
scene = init_plots(['geometry:x','geometry:y'], geo)
rays = []
a = geo.find("m2").a
for i in range(40):
r = Ray(r0=[0.01,a[1],-sqrt(a[0]**2 - a[1]**2)], k=[0,-a[1]/a[0] * (1+ np.random.randn()*0.1) ,1])
#test 1 -0.0359695
#r = Ray(r0=[0,geo.find("m2").a[1],-sqrt(a[0]**2 - a[1]**2)], k=[0,-0.0359695 ,1])
trace_ray(r, geo)
rays.append(r)
'''
f = sqrt(a[0]**2 - a[1]**2)
r = Ray(r0=[0,a[1],-f], k=[0,-a[1]/a[0] ,1])
trace_ray(r, geo)
rays.append(r)
scene.ax[0].plot( [-f,f],[a[1],a[1]],color='red', lw=1)
'''
plot_rays(scene.ax[0], rays, proj='x')
def sseed(input_file,
E_ev,
chicane,
run_dir,
delay=None,
debug=True,
output_file=None,
wake=None,
xt_couple=False,
n_peak=1,
npad=6,
threaded=True):
h = 4.135667516e-15
c = 299792458.0
t1 = time.time()
g = readGenesisOutput(input_file)
print 'read sliced field ', g('ncar'), g.nSlices
ncar = int(g('ncar'))
dgrid = float(g('dgrid'))
idx_max = np.argmax(g.I)
g.idx_max = idx_max
print 'ss: idx_max:', g.idx_max
slices = readRadiationFile(fileName=input_file + '.dfl', npoints=g('ncar'))
print 'field readout :', time.time() - t1, ' sec'
t1 = time.time()
s3d = Signal3D()
s3d.slices = slices
s3d.mesh_size = (int(g('ncar')), int(g('ncar')))
s3d.g = g
pulse3d, bunch = s3d, None
pulse3d.slices = np.reshape(pulse3d.slices, (1, -1)) # 1d array
pulse3d_part = Signal3D()
pulse3d_part.nx = int(pulse3d.g('ncar'))
pulse3d_part.ny = int(pulse3d.g('ncar'))
pulse3d_part.tmax = pulse3d.g.nSlices * pulse3d.g('zsep') * pulse3d.g(
'xlamds') / 2.99792458e8 * 1.e15
pulse3d_part.slices = pulse3d.slices[0]
pulse3d_part.E_ref = 1. / pulse3d.g(
'xlamds') * 4.135667516e-15 * 2.99792458e8
g.npad = npad
pulses_1d = pulses_from_field(pulse3d_part, npad=npad, threaded=threaded)
g.nslice = pulses_1d.nslice
print '*** created', pulses_1d.n_pulses, ' pulses *** '
if debug:
pulse_idx = int(pulse3d_part.nx * pulse3d_part.ny / 2.)
print 'plotting slice', pulse_idx
fig = plt.figure()
ax = fig.add_subplot(221)
ax.grid(True)
ax.plot(pulses_1d.t,
np.abs(pulses_1d.f[pulse_idx]) + 1,
'#000000',
alpha=0.5)
ax.set_title('Stage 1 FEL pulse')
pulse_idx = int(pulse3d_part.nx * pulse3d_part.ny / 2.)
n_fel_start = 0
for i in range(len(pulses_1d.f[pulse_idx])):
if np.abs(pulses_1d.f[pulse_idx][i]) > 1.0:
n_fel_start = i
break
n_points = len(pulses_1d.f[pulse_idx]) / (2 * npad + 1)
g.power_ref = np.abs(pulses_1d.f[pulse_idx])[n_points * npad:n_points *
(npad + 1)]
r = Ray()
r.lamb = 2 * pi * hbar * c / E_ev
print 'wavelength', r.lamb, '(', E_ev, 'eV), filetring...'
filt = get_crystal_filter(chicane.cryst,
r,
ref_idx=chicane.cryst.ref_idx,
k=pulses_1d.freq_k)
print pulses_1d.freq_k
chicane.cryst.filter = filt
f_av = np.zeros(len(pulses_1d.t))
print 'field/filter preparation: ', time.time() - t1, ' sec'
t1 = time.time()
if threaded:
print 'filtering (threaded) ... '
#ncores = multiprocessing.cpu_count()/8
pool = multiprocessing.Pool()
tasks = [
pool.apply_async(filter_1d,
(pulses_1d, chicane.cryst.filter.tr, i))
for i in range(pulses_1d.n_pulses)
]
for t in tasks:
t.wait()
pool.close()
pool.join()
else:
print 'filtering (not threaded) ... '
for i in range(pulses_1d.n_pulses):
#print 'filtering:', i, '/', len(pulses_1d.f[i,:])
filter_1d(pulses_1d, chicane.cryst.filter.tr, i)
for i in xrange(pulses_1d.n_pulses):
f_av += np.abs(pulses_1d.f[i, :])
print 'filtering time: ', time.time() - t1, ' sec'
t1 = time.time()
if wake != None:
f_av = wake
n_marg = 20 / (pulses_1d.t[1] - pulses_1d.t[0]
) # number of margin slices prior to FEL pulse
f_wake = get_wake(f_av, n_fel_start - n_marg, smooth_param=2)
if debug:
ax2 = fig.add_subplot(222)
ax2.set_title('Wake')
ax2.grid(True)
ax2.set_yscale('log')
ax2.plot(f_wake, 'r--')
ax2.plot(f_av, 'g--')
x, y = peaks(pulses_1d.t, f_wake, n=4)
print 'peaks', x, y
if delay == None:
delay = pulses_1d.t[pulses_1d.nslice * npad +
g.idx_max] - x[n_peak] # based on current maximum
n_delay = int(delay / (pulses_1d.t[1] - pulses_1d.t[0]))
n_start = pulses_1d.npad * pulses_1d.nslice - n_delay
print 'delay', delay, ' fs ', delay * 1.e-15 * 3.e8 / 1.e-6, 'mu m ', n_delay, ' slices', ' nslice=', pulses_1d.nslice, ' n_start=', n_start
print 'max current slice: ', pulses_1d.nslice * npad + g.idx_max
i1 = 0
i2 = pulses_1d.n_pulses
t = pulses_1d.t[n_start:n_start + pulses_1d.nslice]
pulse3d.slices = np.reshape(
pulse3d.slices, (pulses_1d.nslice, pulse3d_part.nx, pulse3d_part.nx))
field_from_pulses(t, pulses_1d.f[i1:i2,
n_start:n_start + pulses_1d.nslice],
pulse3d.mesh_size, pulse3d.slices)
g.spec = np.fft.fft(pulse3d.slices[:, ncar / 2, ncar / 2])
g.max_power = np.max(np.abs(pulse3d.slices[:, ncar / 2, ncar / 2]))
g.power = np.abs(pulse3d.slices[:, ncar / 2, ncar / 2])
g.freq_ev = h * fftfreq(len(g.spec), d=(t[1] - t[0]) * 1.e-15)
g.delay = delay
g.seed_axis = np.abs(pulse3d.slices[:, ncar / 2, ncar / 2])
g.wake = f_av
nslice = len(pulse3d.slices[:, 0, 0])
if xt_couple: # spatial-temporal coupling
dct = (pulses_1d.t[1] - pulses_1d.t[0]) * 1.e-15 * c
for i_slice in xrange(len(pulse3d.slices[:, 0, 0])):
#print 'shifting slice', i_slice
shift_x = (nslice - i_slice) * dct * cos(
chicane.cryst.thetaB) / sin(chicane.cryst.thetaB)
#print 'shift_x' , shift_x
#print dgrid, ncar
n_shift = int(shift_x / (dgrid / ncar))
#print 'n_shift', n_shift
pulse3d.slices[i_slice, :, :] = np.roll(
pulse3d.slices[i_slice, :, :], n_shift, 0)
if debug:
ax.set_yscale('log')
ax.plot(t + 0, np.abs(pulse3d.slices[:, ncar / 2, ncar / 2]), 'r--')
ax.plot(t + 0, np.abs(pulse3d.slices[:, ncar / 2, ncar / 2 + 5]),
'r--')
ax.plot(t + delay, np.abs(pulse3d.slices[:, ncar / 2, ncar / 2]), 'g-')
ax.plot(pulses_1d.t[pulses_1d.nslice * npad + g.idx_max],
f_wake[pulses_1d.nslice * npad + g.idx_max], 'bs')
print 'seed t', pulses_1d.t[pulses_1d.nslice * npad +
g.idx_max], f_wake[pulses_1d.nslice * npad
+ g.idx_max]
ax3 = fig.add_subplot(223)
#ax3.plot(t + delay, np.imag(pulse3d.slices[:,ncar/2,ncar/2]), 'b-', lw=1)
print 'debug: max slice', g.idx_max,
ax3.plot(np.abs(pulse3d.slices[100, :, ncar / 2]), 'r--')
ax3.plot(np.abs(pulse3d.slices[200, :, ncar / 2]), 'g--')
ax3.plot(np.abs(pulse3d.slices[300, :, ncar / 2]), 'b--')
ax3.plot(np.abs(pulse3d.slices[g.idx_max, :, ncar / 2]), 'b-')
ax4 = fig.add_subplot(224)
ax4.plot(g.freq_ev, np.abs(g.spec), 'b-')
#plt.title('Spectrum (middle pulse after seed)')
fig = plt.figure()
ax5 = fig.add_subplot(111)
ax5.set_yscale('log')
ax5.plot(np.abs(pulse3d.slices[:, ncar / 2, ncar / 2]), 'r-')
ax5.plot(g.wake[n_start:n_start + pulses_1d.nslice], 'b-')
ax5.plot(g.I, 'g-')
plt.show()
print 'creating final field: ', time.time() - t1, ' sec'
t1 = time.time()
if output_file != None:
writeRadiationFile(output_file + '.dfl', pulse3d.slices)
print 'written radiation file, slices', len(pulse3d.slices[:, ncar / 2,
ncar / 2])
print 'writing final field: ', time.time() - t1, ' sec'
return g
id="m2")
m3 = Mirror(r=[0, -50 * cm, 20 * cm],
size=[10 * cm, 10 * cm, 1 * mm],
pitch_ang=pi / 4.,
id="m3")
m4 = Mirror(r=[0, 0, 20 * cm],
size=[10 * cm, 8 * cm, 10 * mm],
pitch_ang=-3 * pi / 4.,
id="m4")
geo = Geometry([m1, m2, m3, m4])
return geo
geo = init_geometry()
scene = init_plots(['geometry:y'], geo)
rays = []
sigma_y = 0.1e-1 # rad
for i in range(100):
r = Ray(r0=[0, 0, -0.3], k=[0, np.random.randn() * sigma_y, 1])
trace_ray(r, geo)
rays.append(r)
plot_rays(scene.ax[0], rays, proj='y')
plt.show()
no=[0.0, 0, 1],
d=[10 * mum, 10 * mum],
id="a1")
geo = Geometry([m1, a1])
return geo
geo = init_geometry()
scene = init_plots(['geometry:x', 'geometry:y'], geo)
rays = []
a = geo.find("m1").a
r = Ray(r0=[a[1], 0.0, -sqrt(a[0]**2 - a[1]**2)],
k=[-a[1] / a[0] * (1 + 0.0), 0.0, 1])
trace_ray(r, geo)
rays.append(r)
'''
r = Ray(r0=[a[1],0.0, -sqrt(a[0]**2 - a[1]**2)], k=[-a[1]/a[0] * (1 - 0.05) ,0.0, 1])
trace_ray(r, geo)
rays.append(r)
r = Ray(r0=[a[1],0.0, -sqrt(a[0]**2 - a[1]**2)], k=[-a[1]/a[0] * (1 + 0.05) ,0.0, 1])
trace_ray(r, geo)
rays.append(r)
'''
plot_rays(scene.ax[0], rays, proj='x', alpha=1.0)
plot_rays(scene.ax[1], rays, proj='y', alpha=1.0)
geo = init_geometry()
scene = init_plots(['geometry', 'detectors:d1', 'detectors:d2'], geo)
#scene = init_plots(['geometry'], geo)
rays = []
sigma_x = 30.e-2 * mum
sigma_xp = 10.e-16 # rad
sigma_y = 30.e-2 * mum # m
sigma_yp = 10.e-16 # rad
for i in range(1):
r = Ray(r0=[
np.random.randn() * sigma_x,
np.random.randn() * sigma_y, -145 * m
],
k=[np.random.randn() * sigma_xp,
np.random.randn() * sigma_yp, 1])
print('tracing ray...')
trace_ray(r, geo)
rays.append(r)
plot_rays(scene.ax[0], rays)
#plot_detectors(scene, geo)
try:
m1 = geo.find("d1").matrix.transpose()
scene.profile_im["d1"].imshow(m1,
cmap='gist_heat',
interpolation='none',
pitch_ang=3 * pi / 4.,
id="m1")
geo = Geometry([m1])
return geo
geo = init_geometry()
print 'pitch', geo.find("m1").pitch_ang
print 'no', geo.find("m1").no
scene = init_plots(['geometry:y'], geo)
rays = []
r = Ray(r0=[0, 0, -0.6], k=[0, 0, 1])
trace_ray(r, geo)
rays.append(r)
r = Ray(r0=[0, 0, -0.6], k=[0, 0.1, 1])
trace_ray(r, geo)
rays.append(r)
r = Ray(r0=[0, 0, -0.6], k=[0, -0.1, 1])
trace_ray(r, geo)
rays.append(r)
plot_rays(scene.ax[0], rays, proj='y')
plt.show()
size=[0.02 * m, 0.02 * m, 0.20 * m],
d=[10 * mum, 10 * mum],
id="a1")
geo = Geometry([m1, a1])
return geo
geo = init_geometry()
scene = init_plots(['geometry:x', 'geometry:y'], geo)
rays = []
a = geo.find("m1").a
r = Ray(r0=[0.0, a[1], -sqrt(a[0]**2 - a[1]**2)],
k=[0.0, -a[1] / a[0] * (1 + 0.0), 1])
trace_ray(r, geo)
rays.append(r)
r = Ray(r0=[0.0, a[1], -sqrt(a[0]**2 - a[1]**2)],
k=[0.0, -a[1] / a[0] * (1 - 0.05), 1])
trace_ray(r, geo)
rays.append(r)
r = Ray(r0=[0.0, a[1], -sqrt(a[0]**2 - a[1]**2)],
k=[0.0, -a[1] / a[0] * (1 + 0.05), 1])
trace_ray(r, geo)
rays.append(r)
plot_rays(scene.ax[0], rays, proj='x', alpha=1.0)
plot_rays(scene.ax[1], rays, proj='y', alpha=1.0)