def visualize_grating():
beamLine = raycing.BeamLine()
# bg = BlazedGratingAlt(
bg = roe.BlazedGrating(
beamLine,
'BlazedGrating',
(0, p, 0),
pitch=pitch,
material=coating,
blaze=blaze,
#antiblaze=pitch,
rho=rho)
fig1 = plt.figure(figsize=(8, 6), dpi=72)
rect2d = [0.1, 0.1, 0.8, 0.8]
ax = fig1.add_axes(rect2d, aspect='auto')
ax.set_xlabel(u'y (µm)')
ax.set_ylabel(u'z (nm)')
ax.set_title(
u'Grating profile with {0:.0f} lines/mm and {1}° blaze angle\n'.format(
rho, np.degrees(blaze)) +
u'and beam footprint at {0}° pitch angle'.format(np.degrees(pitch)))
maxY = 2.2 * bg.rho_1
y = np.linspace(-2 * maxY, 2 * maxY, 280)
z = bg.local_z(0, y)
ax.plot(y * 1e3, z * 1e6, '-k', lw=2)
beamSource = rs.Beam(nrays=len(y), forceState=1)
beamSourceLoc = rs.Beam(copyFrom=beamSource)
raycing.global_to_virgin_local(bg.bl, beamSource, beamSourceLoc, bg.center,
slice(None))
raycing.rotate_beam(beamSourceLoc, slice(None), pitch=-pitch)
beamSource.z[:] = y * np.tan(pitch)
beamGloSG, beamLoSG = bg.reflect(beamSource)
ax.plot([beamSourceLoc.y * 1e3, beamLoSG.y * 1e3],
[beamSourceLoc.z * 1e6, beamLoSG.z * 1e6],
'-r',
alpha=0.2,
lw=0.5)
ax.plot(beamLoSG.y * 1e3, beamLoSG.z * 1e6, 'or', alpha=0.5, lw=3)
ax.set_xlim(-maxY * 1e3, maxY * 1e3)
mz = bg.rho_1 * np.tan(blaze)
ax.set_ylim(-mz * 1.1e6, mz * 0.2e6)
y1, y2, z1, z2, d = get_grating_area_fraction(rho, blaze, pitch)
xs = np.array([y1, y2]) * 1e3
ys = np.array([z1, z2]) * 1e6
ax.plot(xs, ys, 'og', lw=3)
fig1.savefig(prefix + '_profile.png')
plt.show()
def run_process(beamLine, shineOnly1stSource=False):
beamSource = beamLine.sources[0].shine()
beamFSM0 = beamLine.fsm0.expose(beamSource)
beamTmp = beamLine.feFixedMask.propagate(beamSource)
beamFSMFE = beamLine.fsmFE.expose(beamSource)
beamFilter1global, beamFilter1local1, beamFilter1local2 =\
beamLine.filter1.double_refract(beamSource)
beamFilter1local2A = rs.Beam(copyFrom=beamFilter1local2)
beamFilter1local2A.absorb_intensity(beamSource)
beamFurtherDown = beamFilter1global
beamVCMglobal, beamVCMlocal = beamLine.vcm.reflect(beamFurtherDown)
beamVCMlocal.absorb_intensity(beamFurtherDown)
beamFSMVCM = beamLine.fsmVCM.expose(beamVCMglobal)
outDict = {
'beamSource': beamSource,
'beamFSM0': beamFSM0,
'beamFSMFE': beamFSMFE,
'beamFilter1global': beamFilter1global,
'beamFilter1local1': beamFilter1local1,
'beamFilter1local2': beamFilter1local2,
'beamFilter1local2A': beamFilter1local2A,
'beamVCMglobal': beamVCMglobal,
'beamVCMlocal': beamVCMlocal,
'beamFSMVCM': beamFSMVCM
}
beamLine.beams = outDict
if showIn3D:
beamLine.prepare_flow()
return outDict
def run_process(beamLine):
thetaNodes = (beamLine.orderThetas[:, np.newaxis] + screenThetas).flatten()
waveFSM = beamLine.fsm.prepare_wave(beamLine.bg, screenPhis, thetaNodes)
wrepeats = 1
beamLine.fluxIn = 0
for repeat in range(wrepeats):
beamSource = beamLine.sources[0].shine(withAmplitudes=True)
beamLine.fluxIn += (beamSource.Jss + beamSource.Jpp).sum()
beamGglobal, beamGlocal = beamLine.gr.reflect(beamSource)
beamFSMrays = beamLine.fsm.expose(beamGglobal)
oeGlobal, oeLocal = beamLine.bg.reflect(beamSource)
oeLocal.area = beamLine.bg.area
rw.diffract(oeLocal, waveFSM)
if wrepeats > 1:
print('wave repeats: {0} of {1} done'.format(repeat+1, wrepeats))
beamLine.fluxIn /= wrepeats
beamLine.fluxOut = (oeLocal.Jss + oeLocal.Jpp)[oeLocal.state == 1].sum()
outDict = {'beamSource': beamSource,
'beamGglobal': beamGglobal, 'beamGlocal': beamGlocal,
'beamFSMrays': beamFSMrays,
'waveFSM': waveFSM}
beamLine.waveFSM = waveFSM
oeLocal.y = oeLocal.y % (4*beamLine.bg.rho_1) - 2*beamLine.bg.rho_1
outDict['oeLocal'] = oeLocal
saw = rs.Beam(copyFrom=oeLocal)
saw.y = np.random.uniform(-1.1, 1.1, size=len(saw.x)) * beamLine.bg.rho_1
saw.z = beamLine.bg.local_z(0, saw.y)
outDict['saw'] = saw
return outDict
def align_beamline(HOMS, energy):
SourceBeam = rsources.Beam(nrays=2)
SourceBeam.a[:] = 0
SourceBeam.b[:] = 1
SourceBeam.c[:] = 0
SourceBeam.x[:] = 0
SourceBeam.y[:] = 0
SourceBeam.z[:] = 0
SourceBeam.state[:] = 1
SourceBeam.E[:] = energy
tmpy = HOMS.P1H.center[1]
newx = HOMS.P1H.center[0]
newz = HOMS.P1H.center[2]
HOMS.P1H.center = (newx, tmpy, newz)
print("P1H.center:", HOMS.P1H.center)
P1Hbeam = HOMS.P1H.expose(beam=SourceBeam)
tmpy = HOMS.M1H.center[1]
newx = HOMS.M1H.center[0]
newz = HOMS.M1H.center[2]
HOMS.M1H.center = (newx, tmpy, newz)
print("M1H.center:", HOMS.M1H.center)
M1HBeam, oe01beamLocal01 = HOMS.M1H.reflect(beam=SourceBeam)
tmpy = HOMS.P2H.center[1]
newx = HOMS.P2H.center[0]
newz = HOMS.P2H.center[2]
HOMS.P2H.center = (newx, tmpy, newz)
print("P2H.center:", HOMS.P2H.center)
P2Hbeam = HOMS.P2H.expose(beam=M1HBeam)
tmpy = HOMS.M2H.center[1]
newx = HOMS.M2H.center[0]
newz = HOMS.M2H.center[2]
HOMS.M2H.center = (newx, tmpy, newz)
print("M2H.center:", HOMS.M2H.center)
M2HBeam, oe02beamLocal01 = HOMS.M2H.reflect(beam=M1HBeam)
tmpy = HOMS.P3H.center[1]
newx = HOMS.P3H.center[0]
newz = HOMS.P3H.center[2]
HOMS.P3H.center = (newx, tmpy, newz)
print("P3H.center:", HOMS.P3H.center)
P3HBeam = HOMS.P3H.expose(beam=M2HBeam)
tmpy = HOMS.DG3.center[1]
newx = HOMS.DG3.center[0]
newz = HOMS.DG3.center[2]
HOMS.DG3.center = (newx, tmpy, newz)
print("DG3.center:", HOMS.DG3.center)
DG3Beam = HOMS.DG3.expose(beam=M2HBeam)
def run_process(beamLine):
beamSource = beamLine.sources[0].shine()
beamLine.feFixedMask.propagate(beamSource)
beamFilter1global, beamFilter1local1, beamFilter1local2 = \
beamLine.filter1.double_refract(beamSource)
beamFilter1local2A = rs.Beam(copyFrom=beamFilter1local2)
beamFilter1local2A.absorb_intensity(beamSource)
outDict = {'beamSource': beamSource,
'beamFilter1global': beamFilter1global,
'beamFilter1local1': beamFilter1local1,
'beamFilter1local2': beamFilter1local2,
'beamFilter1local2A': beamFilter1local2A}
beamLine.beams = outDict
return outDict
def run_process(beamLine):
ygloS = beamLine.yglo * (beamLine.E / E_FZP) + p
wavelen = len(ygloS)
wave3Dpoints = rs.Beam(nrays=wavelen, forceState=1, withAmplitudes=True)
rw.prepare_wave(beamLine.fzp, wave3Dpoints, beamLine.xglo, ygloS,
beamLine.zglo)
wave3Dpoints.dS = 1
wrepeats = 1
for repeat in range(wrepeats):
beamSource = beamLine.sources[0].shine(withAmplitudes=True)
outDict = {'beamSource': beamSource}
beamLine.fluxIn = (beamSource.Jss + beamSource.Jpp).sum()
oeGlobal, oeLocal = beamLine.fzp.reflect(beamSource)
oeLocal.area = beamLine.fzp.area
rw.diffract(oeLocal, wave3Dpoints)
if wrepeats > 1:
print('wave repeats: {0} of {1} done'.format(repeat + 1, wrepeats))
beamLine.intensityDiffr = wave3Dpoints.Jss + wave3Dpoints.Jpp
return outDict
def run_process(beamLine, shineOnly1stSource=False):
beamSource = beamLine.sources[0].shine()
# beamLine.feFixedMask.propagate(beamSource)
beamFSM0 = beamLine.fsm0.expose(beamSource)
beamM1global, beamM1local = beamLine.m1.reflect(beamSource)
beamFSM1 = beamLine.fsm1.expose(beamM1global)
beamM2global, beamM2local = beamLine.m2.reflect(beamM1global)
beamPGglobal, beamPGlocal = beamLine.pg.reflect(beamM2global)
beamFSMPG = beamLine.fsmPG.expose(beamPGglobal)
beamM3global, beamM3local = beamLine.m3.reflect(beamPGglobal)
beamFSM3hf = beamLine.fsm3hf.expose(beamM3global)
beamFSM3vf = beamLine.fsm3vf.expose(beamM3global)
outDict = {'beamSource': beamSource,
'beamFSM0': beamFSM0,
'beamM1global': beamM1global, 'beamM1local': beamM1local,
'beamFSM1': beamFSM1,
'beamM2global': beamM2global, 'beamM2local': beamM2local,
'beamPGglobal': beamPGglobal, 'beamPGlocal': beamPGlocal,
'beamFSMPG': beamFSMPG,
'beamM3global': beamM3global, 'beamM3local': beamM3local,
'beamFSM3hf': beamFSM3hf, 'beamFSM3vf': beamFSM3vf,
}
for iopening, s1 in enumerate(beamLine.s1s):
beamM3globalTemp = rs.Beam(copyFrom=beamM3global)
s1.propagate(beamM3globalTemp)
beamFSM3vs = beamLine.fsm3vf.expose(beamM3globalTemp)
beamM4global, beamM4local = beamLine.m4.reflect(beamM3globalTemp)
beamFSMExp1 = beamLine.fsmExp1.expose(beamM4global)
beamFSMExp2 = beamLine.fsmExp2.expose(beamM4global)
sti = '{0:02d}'.format(iopening)
outDict['beamFSM3vsOp'+sti] = beamFSM3vs
outDict['beamM4globalOp'+sti] = beamM4global
outDict['beamM4localOp'+sti] = beamM4local
outDict['beamFSMExp1Op'+sti] = beamFSMExp1
outDict['beamFSMExp2Op'+sti] = beamFSMExp2
return outDict
def run_process(beamLine, shineOnly1stSource=False):
for i in range(len(beamLine.sources)):
curSource = beamLine.sources[i].shine()
if i == 0:
beamSource = curSource
else:
beamSource.concatenate(curSource)
if shineOnly1stSource:
break
beamFSM0 = beamLine.fsm0.expose(beamSource)
beamTmp1 = beamLine.feFixedMask.propagate(beamSource)
beamFSMFE = beamLine.fsmFE.expose(beamSource)
beamFilter1global, beamFilter1local1, beamFilter1local2 = \
beamLine.filter1.double_refract(beamSource)
beamFilter1local2A = rs.Beam(copyFrom=beamFilter1local2)
beamFilter1local2A.absorb_intensity(beamSource)
if hasattr(beamLine, 'filter2'):
beamFilter2global, beamFilter2local1, beamFilter2local2 = \
beamLine.filter2.double_refract(beamFilter1global)
beamFilter2local2.absorb_intensity(beamFilter1global)
beamFurtherDown = beamFilter2global
else:
beamFurtherDown = beamFilter1global
# beamFurtherDown = beamSource
beamVCMglobal, beamVCMlocal = beamLine.vcm.reflect(beamFurtherDown)
beamVCMlocal.absorb_intensity(beamFurtherDown)
beamFSMVCM = beamLine.fsmVCM.expose(beamVCMglobal)
beamDCMglobal, beamDCMlocal1, beamDCMlocal2 = \
beamLine.dcm.double_reflect(beamVCMglobal)
beamDCMlocal1.absorb_intensity(beamVCMglobal)
beamBSBlocklocal = beamLine.BSBlock.propagate(beamDCMglobal)
beamSlitAfterDCMlocal = beamLine.slitAfterDCM.propagate(beamDCMglobal)
beamFSMDCM = beamLine.fsmDCM.expose(beamDCMglobal)
beamVFMglobal, beamVFMlocal = beamLine.vfm.reflect(beamDCMglobal)
beamSlitAfterVFMlocal = beamLine.slitAfterVFM.propagate(beamVFMglobal)
beamFSMVFM = beamLine.fsmVFM.expose(beamVFMglobal)
beamPSLocal = beamLine.ohPS.propagate(beamVFMglobal)
beamSlitEHLocal = beamLine.slitEH.propagate(beamVFMglobal)
beamFSMSample = beamLine.fsmSample.expose(beamVFMglobal)
# 'beamFilter2global': beamFilter2global,
# 'beamFilter2local1': beamFilter2local1,
# 'beamFilter2local2': beamFilter2local2,
outDict = {
'beamSource': beamSource,
'beamFSM0': beamFSM0,
'beamFSMFE': beamFSMFE,
'beamFilter1global': beamFilter1global,
'beamFilter1local1': beamFilter1local1,
'beamFilter1local2': beamFilter1local2,
'beamFilter1local2A': beamFilter1local2A,
'beamVCMglobal': beamVCMglobal,
'beamVCMlocal': beamVCMlocal,
'beamFSMVCM': beamFSMVCM,
'beamDCMglobal': beamDCMglobal,
'beamDCMlocal1': beamDCMlocal1,
'beamDCMlocal2': beamDCMlocal2,
'beamFSMDCM': beamFSMDCM,
'beamBSBlocklocal': beamBSBlocklocal,
'beamSlitAfterDCMlocal': beamSlitAfterDCMlocal,
'beamFSMDCM': beamFSMDCM,
'beamVFMglobal': beamVFMglobal,
'beamVFMlocal': beamVFMlocal,
'beamSlitAfterVFMlocal': beamSlitAfterVFMlocal,
'beamFSMVFM': beamFSMVFM,
'beamPSLocal': beamPSLocal,
'beamSlitEHLocal': beamSlitEHLocal,
'beamFSMSample': beamFSMSample
}
if hasattr(beamLine, 'filter2'):
outDict['beamFilter2global'] = beamFilter2global
outDict['beamFilter2local1'] = beamFilter2local1
outDict['beamFilter2local2'] = beamFilter2local2
beamLine.beams = outDict
if showIn3D:
beamLine.prepare_flow()
return outDict
def shine(self, hitpoint=(0, 10, 0)):
""" Source special logic, shine in direction defined by hitpoint"""
# Obsolete parameters used by the original shine() method
toGlobal = True
withAmplitudes = False
accuBeam = None
# Prepare beam to be returned
bo = rs.Beam(self.nrays, withAmplitudes=withAmplitudes)
bo.state[:] = 1
self._apply_distribution(bo.y, self.disty, self.dy)
# TODO Add normal distribution!
# We want to shine a flat distribution
# around the capillary entrance point
xMin, xMax = hitpoint[0] - self.dx, hitpoint[0] + self.dx
bo.x = np.random.uniform(xMin, xMax, self.nrays)
zMin, zMax = hitpoint[2] - self.dz, hitpoint[2] + self.dz
bo.z = np.random.uniform(zMin, zMax, self.nrays)
# Likewise we want the momentum to be distributed
# around the direction of the capillary entrance
# Only direction of momentum can be specified
# so normalization is mandatory
normfactor = np.sqrt(sum([x**2 for x in hitpoint]))
# With momentum distribution in the x-direction ...
a0 = 1. * hitpoint[0] / normfactor
aMin, aMax = a0 - self.dxprime, a0 + self.dxprime
bo.a = np.random.uniform(aMin, aMax, self.nrays)
# ... and in the z-direction ...
c0 = 1. * hitpoint[2] / normfactor
cMin, cMax = c0 - self.dzprime, c0 + self.dzprime
bo.c = np.random.uniform(cMin, cMax, self.nrays)
# ... we can find the momentum distribution in the y-direction
ac = bo.a**2 + bo.c**2
if sum(ac > 1) > 0:
bo.b[:] = (ac + 1)**0.5
bo.a[:] /= bo.b
bo.c[:] /= bo.b
bo.b[:] = 1.0 / bo.b
else:
bo.b[:] = (1 - ac)**0.5
# This assumes that distE is not None
bo.E[:] = rs.make_energy(self.distE, self.energies,\
self.nrays, self.filamentBeam)
# Add a container for number of reflections for each ray
bo.nRefl = np.zeros_like(bo.state)
# So far we neglect polarization, but it's needed
# for xrt compatibility
rs.make_polarization(self.polarization, bo, self.nrays)
# This assumes toGlobal is True
raycing.virgin_local_to_global(self.bl, bo, self.center)
return bo
def align_beamline(beamLine, energy):
geometricSource01beamGlobal01 = rsources.Beam(nrays=2)
geometricSource01beamGlobal01.a[:] = 0
geometricSource01beamGlobal01.b[:] = 1
geometricSource01beamGlobal01.c[:] = 0
geometricSource01beamGlobal01.x[:] = 0
geometricSource01beamGlobal01.y[:] = 0
geometricSource01beamGlobal01.z[:] = 0
geometricSource01beamGlobal01.E[:] = energy
geometricSource01beamGlobal01.state[:] = 1
tmpy = beamLine.screen02.center[1]
newx = beamLine.screen02.center[0]
newz = beamLine.screen02.center[2]
beamLine.screen02.center = (newx, tmpy, newz)
print("screen02.center:", beamLine.screen02.center)
screen02beamLocal01 = beamLine.screen02.expose(
beam=geometricSource01beamGlobal01)
tmpy = beamLine.lauePlate01.center[1]
newx = beamLine.lauePlate01.center[0]
newz = beamLine.lauePlate01.center[2]
beamLine.lauePlate01.center = (newx, tmpy, newz)
print("lauePlate01.center:", beamLine.lauePlate01.center)
braggT = crystalSi01.get_Bragg_angle(energy)
alphaT = 0 if beamLine.lauePlate01.alpha is None else beamLine.lauePlate01.alpha
lauePitch = 0
print("bragg, alpha:", np.degrees(braggT), np.degrees(alphaT), "degrees")
braggT += -crystalSi01.get_dtheta(energy, alphaT)
if crystalSi01.geom.startswith('Laue'):
lauePitch = 0.5 * np.pi
print("braggT:", np.degrees(braggT), "degrees")
loBeam = rsources.Beam(copyFrom=geometricSource01beamGlobal01)
raycing.global_to_virgin_local(beamLine,
geometricSource01beamGlobal01,
loBeam,
center=beamLine.lauePlate01.center)
raycing.rotate_beam(
loBeam,
roll=-(beamLine.lauePlate01.positionRoll + beamLine.lauePlate01.roll),
yaw=-beamLine.lauePlate01.yaw,
pitch=0)
theta0 = np.arctan2(-loBeam.c[0], loBeam.b[0])
th2pitch = np.sqrt(1. - loBeam.a[0]**2)
targetPitch = np.arcsin(np.sin(braggT) / th2pitch) -\
theta0
targetPitch += alphaT + lauePitch
beamLine.lauePlate01.pitch = targetPitch
print("lauePlate01.pitch:", np.degrees(beamLine.lauePlate01.pitch),
"degrees")
lauePlate01beamGlobal01, lauePlate01beamLocal01 = beamLine.lauePlate01.reflect(
beam=geometricSource01beamGlobal01)
print "Laue Plate exit point"
print lauePlate01beamGlobal01.x, lauePlate01beamGlobal01.y, lauePlate01beamGlobal01.z
tmpy = beamLine.screen01.center[1]
newx = lauePlate01beamGlobal01.x[0] +\
lauePlate01beamGlobal01.a[0] * (tmpy - lauePlate01beamGlobal01.y[0]) /\
lauePlate01beamGlobal01.b[0]
newz = lauePlate01beamGlobal01.z[0] +\
lauePlate01beamGlobal01.c[0] * (tmpy - lauePlate01beamGlobal01.y[0]) /\
lauePlate01beamGlobal01.b[0]
beamLine.screen01.center = (newx, tmpy, newz)
print("screen01.center:", beamLine.screen01.center)
screen01beamLocal01 = beamLine.screen01.expose(
beam=lauePlate01beamGlobal01)
def visualize_grating():
from matplotlib.patches import Arc
beamLine = raycing.BeamLine()
bg = roe.BlazedGrating(
beamLine, 'BlazedGrating', (0, p, 0), pitch=pitch, material=coating,
blaze=blaze,
#antiblaze=pitch,
rho=rho,
# gratingDensity=['y', rho, 1, 0, 1e-7]
)
fig1 = plt.figure(figsize=(8, 6), dpi=100)
rect2d = [0.1, 0.1, 0.8, 0.8]
ax = fig1.add_axes(rect2d, aspect='auto')
ax.set_xlabel(u'y (µm)')
ax.set_ylabel(u'z (nm)')
ax.set_title(
u'Grating profile with {0:.0f} lines/mm and {1:.2f}° blaze angle\n'.format(
rho, np.degrees(blaze)) +
u'and beam footprint at {0}° pitch angle'.format(np.degrees(pitch)))
maxY = 2.2 * bg.rho_1
y = np.linspace(-2*maxY, 2*maxY, 1000)
z = bg.local_z(0, y)
ax.plot(y*1e3, z*1e6, '-k', lw=2)
y = np.linspace(-2*maxY, 2*maxY, 300)
z = bg.local_z(0, y)
beamSource = rs.Beam(nrays=len(y), forceState=1)
beamSourceLoc = rs.Beam(copyFrom=beamSource)
raycing.global_to_virgin_local(bg.bl, beamSource, beamSourceLoc,
bg.center, slice(None))
raycing.rotate_beam(beamSourceLoc, slice(None), pitch=-pitch)
beamSource.z[:] = y * np.tan(pitch)
beamGloSG, beamLoSG = bg.reflect(beamSource)
ax.plot([beamSourceLoc.y*1e3, beamLoSG.y*1e3],
[beamSourceLoc.z*1e6, beamLoSG.z*1e6], '-r', alpha=0.2, lw=0.5)
ax.plot(beamLoSG.y*1e3, beamLoSG.z*1e6, 'or', alpha=0.5, lw=3)
ax.set_xlim(-maxY*1e3, maxY*1e3)
mz = bg.rho_1*np.tan(blaze)
ax.set_ylim(-mz*1.1e6, mz*0.2e6)
# y1, y2, z1, z2, d = get_grating_area_fraction(rho, blaze, pitch)
# xs = np.array([y1, y2]) * 1e3
# ys = np.array([z1, z2]) * 1e6
# ax.plot(xs, ys, 'og', lw=3)
if bg.gratingDensity is not None:
ax.plot(bg.ticks*1e3, np.zeros_like(bg.ticks), 'og', lw=3)
ax.plot([-0.5, 2.2], [-mz*1e6, -mz*1e6], alpha=0.5, lw=1)
ax.add_patch(Arc([0, -mz*1e6], maxY*0.22e3, mz*0.2e6, theta1=0,
theta2=90-blazeDeg, color='b'))
ax.add_patch(Arc([bg.rho_1*1e3, -mz*1e6], maxY*0.22e3, mz*0.2e6, theta1=90,
theta2=180, color='b'))
ax.text(bg.rho_1*0.15e3, -mz*0.9e6, 'blaze', ha='left', va='center',
fontsize=12, color='b')
ax.text(bg.rho_1*0.97e3, -mz*0.83e6, 'anti-\nblaze', ha='right', va='center',
fontsize=12, color='b')
fig1.savefig(prefix + '_profile.png')
plt.show()
